Editorial

8 pages, 251 KiB

Open AccessEditorial

by Pierre Sourdille and Pierre Devaux

Biology 2022, 11(10), 1373; https://doi.org/10.3390/biology11101373 - 20 Sep 2022

Cited by 1 | Viewed by 1496

Improving the production of all crops is crucial to meeting the challenge of the growing needs related to the simultaneous increase in the world population and demands from farmers and end-users [...] Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

3 pages, 208 KiB

Open AccessEditorial

Crop Improvement: Now and Beyond

by Pierre Sourdille and Pierre Devaux

Biology 2021, 10(5), 421; https://doi.org/10.3390/biology10050421 - 10 May 2021

Cited by 2 | Viewed by 2256

Abstract

There is an urgent need to increase and improve the production of most agronomic species to meet the current food security challenge [...] Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

Research

Jump to: Editorial, Review, Other

22 pages, 2446 KiB

Open AccessArticle

Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview

by Martin Spanoghe, Thierry Marique, Alexandra Nirsha, Florence Esnault and Deborah Lanterbecq

Biology 2022, 11(4), 604; https://doi.org/10.3390/biology11040604 - 15 Apr 2022

Cited by 6 | Viewed by 2600

Abstract

We investigated the changes in genetic diversity over time and space of the cultivated potato (Solanum tuberosum L.) for the period pre-1800 to 2021. A substantial panel of 1219 potato varieties, belonging to different spatiotemporal groups, was examined using a set of [...] Read more.

We investigated the changes in genetic diversity over time and space of the cultivated potato (Solanum tuberosum L.) for the period pre-1800 to 2021. A substantial panel of 1219 potato varieties, belonging to different spatiotemporal groups, was examined using a set of 35 microsatellite markers (SSR). Genotypic data covering a total of 407 alleles was analyzed using both self-organizing map (SOM) and discriminant analysis of principal components (DAPC) de novo and a priori clustering methods, respectively. Data analysis based on different models of genetic structuring provided evidence of (1) at least two early lineages that have been maintained since their initial introduction from the Andes into Europe in the 16th century, followed by later ones coming from reintroduction events from the US in the mid-1800s; (2) a level of diversity that has gradually evolved throughout the studied time periods and areas, with the most modern variety groups encompassing most of the diversity found in earlier decades; (3) the emergence of new genetic groups within the current population due to increases in the use of germplasm enhancement practices using exotic germplasms. In addition, analysis revealed significant genetic differentiation both among and within the spatiotemporal groups of germplasm studied. Our results therefore highlight that no major genetic narrowing events have occurred within the cultivated potato over the past three centuries. On the contrary, the genetic base shows promising signs of improvement, thanks to extensive breeding work that is gaining momentum. This overview could be drawn on not only to understand better how past decisions have impacted the current genetic cultivated potato resources, but also to develop appropriate new strategies for breeding programs consistent with the socio-economic and sustainability challenges faced by agrifood systems. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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20 pages, 2731 KiB

Open AccessArticle

Reaping the Potential of Wild Cajanus Species through Pre-Breeding for Improving Resistance to Pod Borer, Helicoverpa armigera, in Cultivated Pigeonpea (Cajanus cajan (L.) Millsp.)

by Shivali Sharma, Jagdish Jaba, Polneni Jaganmohan Rao, Suraj Prasad, Nammi Tripura Venkata Venu Gopal, Hari Chand Sharma and Benjamin Kilian

Biology 2022, 11(4), 485; https://doi.org/10.3390/biology11040485 - 22 Mar 2022

Cited by 3 | Viewed by 2000

Abstract

Pod borer (Helicoverpa armigera) causes the highest yield losses in pigeonpea, followed by pod fly (Melanagromyza obtusa). High levels of resistance to pod borer are not available in the cultivated genepool. Several accessions of wild Cajanus species with strong [...] Read more.

Pod borer (Helicoverpa armigera) causes the highest yield losses in pigeonpea, followed by pod fly (Melanagromyza obtusa). High levels of resistance to pod borer are not available in the cultivated genepool. Several accessions of wild Cajanus species with strong resistance, and different resistance mechanisms (antixenosis and antibiosis) to pod borer have been identified. These accessions can be utilized to improve the pod borer resistance of cultivated pigeonpea. Using pod borer resistant Cajanus scarabaeoides and Cajanus acutifolius as pollen donors and popular pigeonpea varieties as recipients, pre-breeding populations were developed following simple- and complex-cross approaches. Preliminary evaluation of four backcross populations consisting of >2300 introgression lines (ILs) under un-sprayed field conditions resulted in identifying 156 ILs with low visual damage rating scores (5.0–6.0) and low pod borer damage (<50%). Precise re-screening of these ILs over different locations and years resulted in the identification of 21 ILs having improved resistance to pod borer. Because these ILs were derived from wild Cajanus species, they may contain different alleles for different resistance components to pod borer. Hence, these ILs are ready-to-use novel and diverse sources of pod borer resistance that can be utilized for improving the pod borer resistance of cultivated pigeonpea. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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17 pages, 3678 KiB

Open AccessEditor’s ChoiceArticle

Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne Rhizoctonia solani AG-2-2-IIIB Resistance in Sugar Beet

by Samathmika Ravi, Mahdi Hassani, Bahram Heidari, Saptarathi Deb, Elena Orsini, Jinquan Li, Christopher M. Richards, Lee W. Panella, Subhashini Srinivasan, Giovanni Campagna, Giuseppe Concheri, Andrea Squartini and Piergiorgio Stevanato

Biology 2022, 11(1), 49; https://doi.org/10.3390/biology11010049 - 29 Dec 2021

Cited by 7 | Viewed by 3516

Abstract

Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide [...] Read more.

Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide polymorphism (SNP) marker linked to Rhizoctonia resistance using restriction site-associated DNA (RAD) sequencing of two geographically discrete sets of plant materials with different degrees of resistance/susceptibility to enable a wider selection of superior genotypes. The variant calling pipeline utilized SAMtools for variant calling and the resulting raw SNPs from RAD sequencing (15,988 and 22,439 SNPs) were able to explain 13.40% and 25.45% of the phenotypic variation in the two sets of material from different sources of origin, respectively. An association analysis was carried out independently on both the datasets and mutually occurring significant SNPs were filtered depending on their contribution to the phenotype using principal component analysis (PCA) biplots. To provide a ready-to-use marker for the breeding community, a systematic molecular validation of significant SNPs distributed across the genome was undertaken to combine high-resolution melting, Sanger sequencing, and rhAmp SNP genotyping. We report that RsBv1 located on Chromosome 6 (9,000,093 bp) is significantly associated with Rhizoctonia resistance (p < 0.01) and able to explain 10% of the phenotypic disease variance. The related SNP assay is thus ready for marker-assisted selection in sugar beet breeding for Rhizoctonia resistance. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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22 pages, 1735 KiB

Open AccessArticle

Characterization and Use in Wheat Breeding of Leaf Rust Resistance Genes from Durable Varieties

by María José Diéguez, Micaela López, Emiliano Altieri, María Fernanda Pergolesi, Marisol Alicia Dabove, Alba Romina Cuyeu, Nadia Justus, Mariana Kandus, Lorena Ingala and Francisco Sacco

Biology 2021, 10(11), 1168; https://doi.org/10.3390/biology10111168 - 12 Nov 2021

Cited by 2 | Viewed by 2564

Abstract

Leaf rust is one of the most significant diseases of wheat worldwide. In Argentina, it is one of the main reasons for variety replacement that becomes susceptible after large-scale use. Some varieties showed durable resistance to this disease, including Buck Manantial and Sinvalocho [...] Read more.

Leaf rust is one of the most significant diseases of wheat worldwide. In Argentina, it is one of the main reasons for variety replacement that becomes susceptible after large-scale use. Some varieties showed durable resistance to this disease, including Buck Manantial and Sinvalocho MA. RILs (Recombinant Inbred Lines) were developed for each of these varieties and used in genetics studies to identify components of resistance, both in greenhouse inoculations using leaf rust races, and in field evaluations under natural population infections. In Buck Manantial, the APR gene LrBMP1 was associated with resistance in field tests. In crosses involving Sinvalocho MA, four genes were previously identified and associated with resistance in field testing: APR (Adult Plant Resistance) gene LrSV1, the APR genetic system LrSV2 + LrcSV2 and the ASR (All Stage Resistance) gene LrG6. Using backcrosses, LrBMP1 was introgressed in four commercial susceptible varieties and LrSV1, LrSV2 + LrcSV2 and LrG6 were simultaneously introgressed in three susceptible commercial varieties. The use of molecular markers for recurrent parent background selection allowed us to select resistant lines with more than 80% similarity to commercial varieties. Additionally, progress towards positional cloning of the genetic system LrSV2 + LrcSV2 for leaf rust APR is reported. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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17 pages, 6157 KiB

Open AccessArticle

Systematic Characterization of TCP Gene Family in Four Cotton Species Revealed That GhTCP62 Regulates Branching in Arabidopsis

by Zhao Liu, Jingyu Yang, Shengdong Li, Le Liu, Ghulam Qanmber, Guoquan Chen, Zhenyu Duan, Na Zhao and Gang Wang

Biology 2021, 10(11), 1104; https://doi.org/10.3390/biology10111104 - 26 Oct 2021

Cited by 11 | Viewed by 2160

Abstract

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play an essential role in regulating various physiological and biochemical functions during plant growth. However, the function of TCP transcription factors in G. hirsutum has not yet been studied. In this study, we performed genome-wide identification and correlation [...] Read more.

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play an essential role in regulating various physiological and biochemical functions during plant growth. However, the function of TCP transcription factors in G. hirsutum has not yet been studied. In this study, we performed genome-wide identification and correlation analysis of the TCP transcription factor family in G. hirsutum. We identified 72 non-redundant GhTCP genes and divided them into seven subfamilies, based on phylogenetic analysis. Most GhTCP genes in the same subfamily displayed similar exon and intron structures and featured highly conserved motif structures in their subfamily. Additionally, the pattern of chromosomal distribution demonstrated that GhTCP genes were unevenly distributed on 24 out of 26 chromosomes, and that fragment replication was the main replication event of GhTCP genes. In TB1 sub-family genes, GhTCP62 was highly expressed in the axillary buds, suggesting that GhTCP62 significantly affected cotton branching. Additionally, subcellular localization results indicated that GhTCP62 is located in the nucleus and possesses typical transcription factor characteristics. The overexpression of GhTCP62 in Arabidopsis resulted in fewer rosette-leaf branches and cauline-leaf branches. Furthermore, the increased expression of HB21 and HB40 genes in Arabidopsis plants overexpressing GhTCP62 suggests that GhTCP62 may regulate branching by positively regulating HB21 and HB40. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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15 pages, 2550 KiB

Open AccessArticle

Comparative Phenotypic and Agronomic Assessment of Transgenic Potato with 3R-Gene Stack with Complete Resistance to Late Blight Disease

by Arinaitwe Abel Byarugaba, Gerald Baguma, Douglas Mutebi Jjemba, Aharinta Kenneth Faith, Arthur Wasukira, Eric Magembe, Anne Njoroge, Alex Barekye and Marc Ghislain

Biology 2021, 10(10), 952; https://doi.org/10.3390/biology10100952 - 23 Sep 2021

Cited by 7 | Viewed by 2552

Abstract

Transgenic potato event Vic.172, expressing three naturally occurring resistance genes (R genes) conferring complete protection against late blight disease, was evaluated for resistance to late blight, phenotypic characterization, and agronomic performance in field conditions at three locations during three seasons in Uganda. [...] Read more.

Transgenic potato event Vic.172, expressing three naturally occurring resistance genes (R genes) conferring complete protection against late blight disease, was evaluated for resistance to late blight, phenotypic characterization, and agronomic performance in field conditions at three locations during three seasons in Uganda. These trials were conducted by comparison to the variety Victoria from which Vic.172 derives, using identical fungicide treatment, except when evaluating disease resistance. During all seasons, the transgenic event Vic.172 was confirmed to have complete resistance to late blight disease, whereas Victoria plants were completely dead by 60–80 days after planting. Tubers from Vic.172 were completely resistant to LB after artificial inoculation. The phenotypic characterization included observations of the characteristics and development of the stems, leaves, flowers, and tubers. Differences in phenotypic parameters between Vic.172 and Victoria were not statistically significant across locations and seasons. The agronomic performance observations covered sprouting, emergence, vigor, foliage growth, and yield. Differences in agronomic performance were not statistically significant except for marketable yield in one location under high productivity conditions. However, yield variation across locations and seasons was not statistically significant, but was influenced by the environment. Hence, the results of the comparative assessment of the phenotype and agronomic performance revealed that transgenic event Vic.172 did not present biologically significant differences in comparison to the variety Victoria it derives from. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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20 pages, 5689 KiB

Open AccessArticle

Dissecting Bread Wheat Heterosis through the Integration of Agronomic and Physiological Traits

by Kevin Gimenez, Pierre Blanc, Odile Argillier, Jean-Baptiste Pierre, Jacques Le Gouis and Etienne Paux

Biology 2021, 10(9), 907; https://doi.org/10.3390/biology10090907 - 13 Sep 2021

Cited by 8 | Viewed by 2521

Abstract

To meet the challenge of feeding almost 10 billion people by 2050, wheat yield has to double by 2050. However, over the past 20 years, yield increase has slowed down and even stagnated in the main producing countries. Following the example of maize, [...] Read more.

To meet the challenge of feeding almost 10 billion people by 2050, wheat yield has to double by 2050. However, over the past 20 years, yield increase has slowed down and even stagnated in the main producing countries. Following the example of maize, hybrids have been suggested as a solution to overcome yield stagnation in wheat. However, wheat heterosis is still limited and poorly understood. Gaining a better understanding of hybrid vigor holds the key to breed for better varieties. To this aim, we have developed and phenotyped for physiological and agronomic traits an incomplete factorial design consisting of 91 hybrids and their nineteen female and sixteen male parents. Monitoring the plant development with normalized difference vegetation index revealed that 89% of the hybrids including the five higher yielding hybrids had a longer grain filling phase with a delayed senescence that results in larger grain size. This average increase of 7.7% in thousand kernel weight translated to a positive mid-parent heterosis for grain yield for 86% of hybrids. In addition, hybrids displayed a positive grain protein deviation leading to a +4.7% heterosis in protein yield. These results shed light on the physiological bases underlying yield heterosis in wheat, paving new ways to breed for better wheat hybrids. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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13 pages, 1958 KiB

Open AccessArticle

Qualitative and Quantitative Resistance against Early Blight Introgressed in Potato

by Pieter J. Wolters, Doret Wouters, Emil J. Kromhout, Dirk Jan Huigen, Richard G. F. Visser and Vivianne G. A. A. Vleeshouwers

Biology 2021, 10(9), 892; https://doi.org/10.3390/biology10090892 - 10 Sep 2021

Cited by 11 | Viewed by 2722

Abstract

Early blight is a disease of potato that is caused by Alternaria species, notably A. solani. The disease is usually controlled with fungicides. However, A. solani is developing resistance against fungicides, and potato cultivars with genetic resistance to early blight are currently [...] Read more.

Early blight is a disease of potato that is caused by Alternaria species, notably A. solani. The disease is usually controlled with fungicides. However, A. solani is developing resistance against fungicides, and potato cultivars with genetic resistance to early blight are currently not available. Here, we identify two wild potato species, which are both crossable with cultivated potato (Solanum tuberosum), that show promising resistance against early blight disease. The cross between resistant S. berthaultii and a susceptible diploid S. tuberosum gave rise to a population in which resistance was inherited quantitatively. S. commersonii subsp. malmeanum was also crossed with diploid S. tuberosum, despite a differing endosperm balance number. This cross resulted in triploid progeny in which resistance was inherited dominantly. This is somewhat surprising, as resistance against necrotrophic plant pathogens is usually a quantitative trait or inherited recessively according to the inverse-gene-for-gene model. Hybrids with high levels of resistance to early blight are present among progeny from S. berthaultii as well as S. commersonii subsp. malmeanum, which is an important step towards the development of a cultivar with natural resistance to early blight. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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19 pages, 3584 KiB

Open AccessArticle

Effect of Flowering Time-Related Genes on Biomass, Harvest Index, and Grain Yield in CIMMYT Elite Spring Bread Wheat

by Susanne Dreisigacker, Juan Burgueño, Angela Pacheco, Gemma Molero, Sivakumar Sukumaran, Carolina Rivera-Amado, Matthew Reynolds and Simon Griffiths

Biology 2021, 10(9), 855; https://doi.org/10.3390/biology10090855 - 01 Sep 2021

Cited by 12 | Viewed by 3920

Abstract

Grain yield (YLD) is a function of the total biomass (BM) and of partitioning the biomass by grains, i.e., the harvest index (HI). The most critical developmental stage for their determination is the flowering time, which mainly depends on the vernalization requirement ( [...] Read more.

Grain yield (YLD) is a function of the total biomass (BM) and of partitioning the biomass by grains, i.e., the harvest index (HI). The most critical developmental stage for their determination is the flowering time, which mainly depends on the vernalization requirement (Vrn) and photoperiod sensitivity genes (Ppd) loci. Allelic variants at the Vrn, Ppd, and earliness per se (Eps) genes of elite spring wheat genotypes included in High Biomass Association Panel (HiBAP) I and II were used to estimate their effects on the phenological stages BM, HI, and YLD. Each panel was grown for two consecutive years in Northwest Mexico. Spring alleles at Vrn-1 had the largest effect on shortening the time to anthesis, and the Ppd-insensitive allele Ppd-D1a had the most significant positive effect on YLD in both panels. In addition, alleles at TaTOE-B1 and TaFT3-B1 promoted between 3.8% and 7.6% higher YLD and 4.2% and 10.2% higher HI in HiBAP I and II, respectively. When the possible effects of the TaTOE-B1 and TaFT3-B1 alleles on the sink and source traits were explored, the favorable allele at TaTOE-B1 showed positive effects on several sink traits mainly related to grain number. The favorable alleles at TaFT3-B1 followed a different pattern, with positive effects on the traits related to grain weight. The results of this study expanded the wheat breeders’ toolbox in the quest to breed better-adapted and higher-yielding wheat cultivars. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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17 pages, 5437 KiB

Open AccessArticle

A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency

by Franz Boideau, Alexandre Pelé, Coleen Tanguy, Gwenn Trotoux, Frédérique Eber, Loeiz Maillet, Marie Gilet, Maryse Lodé-Taburel, Virginie Huteau, Jérôme Morice, Olivier Coriton, Cyril Falentin, Régine Delourme, Mathieu Rousseau-Gueutin and Anne-Marie Chèvre

Biology 2021, 10(8), 771; https://doi.org/10.3390/biology10080771 - 13 Aug 2021

Cited by 8 | Viewed by 3177

Abstract

Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more [...] Read more.

Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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17 pages, 30957 KiB

Open AccessArticle

Evaluation of Genomic Prediction for Fusarium Head Blight Resistance with a Multi-Parental Population

by Wentao Zhang, Kerry Boyle, Anita Brule-Babel, George Fedak, Peng Gao, Zeinab Robleh Djama, Brittany Polley, Richard Cuthbert, Harpinder Randhawa, Robert Graf, Fengying Jiang, Francois Eudes and Pierre R. Fobert

Biology 2021, 10(8), 756; https://doi.org/10.3390/biology10080756 - 06 Aug 2021

Cited by 8 | Viewed by 2594

Abstract

Fusarium head blight (FHB) resistance is quantitatively inherited, controlled by multiple minor effect genes, and highly affected by the interaction of genotype and environment. This makes genomic selection (GS) that uses genome-wide molecular marker data to predict the genetic breeding value as a [...] Read more.

Fusarium head blight (FHB) resistance is quantitatively inherited, controlled by multiple minor effect genes, and highly affected by the interaction of genotype and environment. This makes genomic selection (GS) that uses genome-wide molecular marker data to predict the genetic breeding value as a promising approach to select superior lines with better resistance. However, various factors can affect accuracies of GS and better understanding how these factors affect GS accuracies could ensure the success of applying GS to improve FHB resistance in wheat. In this study, we performed a comprehensive evaluation of factors that affect GS accuracies with a multi-parental population designed for FHB resistance. We found larger sample sizes could get better accuracies. Training population designed by CDmean based optimization algorithms significantly increased accuracies than random sampling approach, while mean of predictor error variance (PEVmean) had the poorest performance. Different genomic selection models performed similarly for accuracies. Including prior known large effect quantitative trait loci (QTL) as fixed effect into the GS model considerably improved the predictability. Multi-traits models had almost no effects, while the multi-environment model outperformed the single environment model for prediction across different environments. By comparing within and across family prediction, better accuracies were obtained with the training population more closely related to the testing population. However, achieving good accuracies for GS prediction across populations is still a challenging issue for GS application. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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17 pages, 1245 KiB

Open AccessArticle

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

by Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne-Marie Chèvre, Patrick Wincker, Mathieu Rousseau-Gueutin and Jean-Marc Aury

Biology 2021, 10(8), 732; https://doi.org/10.3390/biology10080732 - 30 Jul 2021

Cited by 13 | Viewed by 4606

Abstract

With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is [...] Read more.

With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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16 pages, 1630 KiB

Open AccessArticle

Efficiency of a Seedling Phenotyping Strategy to Support European Wheat Breeding Focusing on Leaf Rust Resistance

by Ulrike Beukert, Nina Pfeiffer, Erhard Ebmeyer, Valentin Hinterberger, Stefanie Lueck, Albrecht Serfling, Frank Ordon, Albert Wilhelm Schulthess and Jochen Christoph Reif

Biology 2021, 10(7), 628; https://doi.org/10.3390/biology10070628 - 06 Jul 2021

Cited by 4 | Viewed by 2554

Abstract

Leaf rust resistance is of high importance for a sustainable European wheat production. The expression of known resistance genes starts at different developmental stages of wheat. Breeding for resistance can be supported by a fast, precise, and resource-saving phenotyping. The examination of detached [...] Read more.

Leaf rust resistance is of high importance for a sustainable European wheat production. The expression of known resistance genes starts at different developmental stages of wheat. Breeding for resistance can be supported by a fast, precise, and resource-saving phenotyping. The examination of detached leaf assays of juvenile plants inoculated under controlled conditions and phenotyped by a robotic- and computer-based, high-throughput system is a promising approach in this respect. Within this study, the validation of the phenotyping workflow was conducted based on a winter wheat set derived from Central Europe and examined at different plant developmental stages. Moderate Pearson correlations of 0.38–0.45 comparing leaf rust resistance of juvenile and adult plants were calculated and may be mainly due to different environmental conditions. Specially, the infection under controlled conditions was limited by the application of a single rust race at only one time point. Our results suggest that the diversification with respect to the applied rust race spectrum is promising to increase the consistency of detached leaf assays and the transferability of its results to the field. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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20 pages, 3354 KiB

Open AccessEditor’s ChoiceArticle

A Duplicated Copy of the Meiotic Gene ZIP4 Preserves up to 50% Pollen Viability and Grain Number in Polyploid Wheat

by Abdul Kader Alabdullah, Graham Moore and Azahara C. Martín

Biology 2021, 10(4), 290; https://doi.org/10.3390/biology10040290 - 02 Apr 2021

Cited by 8 | Viewed by 4791

Abstract

Although most flowering plants are polyploid, little is known of how the meiotic process evolves after polyploidisation to stabilise and preserve fertility. On wheat polyploidisation, the major meiotic gene ZIP4 on chromosome 3B duplicated onto 5B and diverged (TaZIP4-B2). TaZIP4-B2 was [...] Read more.

Although most flowering plants are polyploid, little is known of how the meiotic process evolves after polyploidisation to stabilise and preserve fertility. On wheat polyploidisation, the major meiotic gene ZIP4 on chromosome 3B duplicated onto 5B and diverged (TaZIP4-B2). TaZIP4-B2 was recently shown to promote homologous pairing, synapsis and crossover, and suppress homoeologous crossover. We therefore suspected that these meiotic stabilising effects could be important for preserving wheat fertility. A CRISPR Tazip4-B2 mutant was exploited to assess the contribution of the 5B duplicated ZIP4 copy in maintaining pollen viability and grain setting. Analysis demonstrated abnormalities in 56% of meiocytes in the Tazip4-B2 mutant, with micronuclei in 50% of tetrads, reduced size in 48% of pollen grains and a near 50% reduction in grain number. Further studies showed that most of the reduced grain number occurred when Tazip4-B2 mutant plants were pollinated with the less viable Tazip4-B2 mutant pollen rather than with wild type pollen, suggesting that the stabilising effect of TaZIP4-B2 on meiosis has a greater consequence in subsequent male, rather than female gametogenesis. These studies reveal the extraordinary value of the wheat chromosome 5B TaZIP4-B2 duplication to agriculture and human nutrition. Future studies should further investigate the role of TaZIP4-B2 on female fertility and assess whether different TaZIP4-B2 alleles exhibit variable effects on meiotic stabilisation and/or resistance to temperature change. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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Review

Jump to: Editorial, Research, Other

15 pages, 1451 KiB

Open AccessReview

Manipulation of Meiotic Recombination to Hasten Crop Improvement

by Ian Fayos, Julien Frouin, Donaldo Meynard, Aurore Vernet, Léo Herbert and Emmanuel Guiderdoni

Biology 2022, 11(3), 369; https://doi.org/10.3390/biology11030369 - 25 Feb 2022

Cited by 5 | Viewed by 3356

Abstract

Reciprocal (cross-overs = COs) and non-reciprocal (gene conversion) DNA exchanges between the parental chromosomes (the homologs) during meiotic recombination are, together with mutation, the drivers for the evolution and adaptation of species. In plant breeding, recombination combines alleles from genetically diverse accessions to [...] Read more.

Reciprocal (cross-overs = COs) and non-reciprocal (gene conversion) DNA exchanges between the parental chromosomes (the homologs) during meiotic recombination are, together with mutation, the drivers for the evolution and adaptation of species. In plant breeding, recombination combines alleles from genetically diverse accessions to generate new haplotypes on which selection can act. In recent years, a spectacular progress has been accomplished in the understanding of the mechanisms underlying meiotic recombination in both model and crop plants as well as in the modulation of meiotic recombination using different strategies. The latter includes the stimulation and redistribution of COs by either modifying environmental conditions (e.g., T°), harnessing particular genomic situations (e.g., triploidy in Brassicaceae), or inactivating/over-expressing meiotic genes, notably some involved in the DNA double-strand break (DSB) repair pathways. These tools could be particularly useful for shuffling diversity in pre-breeding generations. Furthermore, thanks to the site-specific properties of genome editing technologies the targeting of meiotic recombination at specific chromosomal regions nowadays appears an attainable goal. Directing COs at desired chromosomal positions would allow breaking linkage situations existing between favorable and unfavorable alleles, the so-called linkage drag, and accelerate genetic gain. This review surveys the recent achievements in the manipulation of meiotic recombination in plants that could be integrated into breeding schemes to meet the challenges of deploying crops that are more resilient to climate instability, resistant to pathogens and pests, and sparing in their input requirements. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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14 pages, 2200 KiB

Open AccessReview

Breeding More Crops in Less Time: A Perspective on Speed Breeding

by Kajal Samantara, Abhishek Bohra, Sourav Ranjan Mohapatra, Riry Prihatini, Flora Asibe, Lokendra Singh, Vincent P. Reyes, Abha Tiwari, Alok Kumar Maurya, Janine S. Croser, Shabir Hussain Wani, Kadambot H. M. Siddique and Rajeev K. Varshney

Biology 2022, 11(2), 275; https://doi.org/10.3390/biology11020275 - 10 Feb 2022

Cited by 36 | Viewed by 14337

Abstract

Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, [...] Read more.

Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, speed breeding (SB), relying mainly on photoperiod extension, temperature control, and early seed harvest, has the potential to accelerate the rate of plant improvement. Well demonstrated in the case of long-day plants, the SB protocols are being extended to short-day plants to reduce the generation interval time. Flexibility in SB protocols allows them to align and integrate with diverse research purposes including population development, genomic selection, phenotyping, and genomic editing. In this review, we discuss the different SB methodologies and their application to hasten future plant improvement. Though SB has been extensively used in plant phenotyping and the pyramiding of multiple traits for the development of new crop varieties, certain challenges and limitations hamper its widespread application across diverse crops. However, the existing constraints can be resolved by further optimization of the SB protocols for critical food crops and their efficient integration in plant breeding pipelines. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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28 pages, 2986 KiB

Open AccessReview

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection

by Etienne Paux, Stéphane Lafarge, François Balfourier, Jérémy Derory, Gilles Charmet, Michael Alaux, Geoffrey Perchet, Marion Bondoux, Frédéric Baret, Romain Barillot, Catherine Ravel, Pierre Sourdille, Jacques Le Gouis and on behalf of the BREEDWHEAT Consortium

Biology 2022, 11(1), 149; https://doi.org/10.3390/biology11010149 - 17 Jan 2022

Cited by 4 | Viewed by 4853

Abstract

There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools [...] Read more.

There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker–trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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31 pages, 1964 KiB

Open AccessReview

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

by Gargi Prasad Saradadevi, Debajit Das, Satendra K. Mangrauthia, Sridev Mohapatra, Channakeshavaiah Chikkaputtaiah, Manish Roorkiwal, Manish Solanki, Raman Meenakshi Sundaram, Neeraja N. Chirravuri, Akshay S. Sakhare, Suneetha Kota, Rajeev K. Varshney and Gireesha Mohannath

Biology 2021, 10(12), 1255; https://doi.org/10.3390/biology10121255 - 01 Dec 2021

Cited by 10 | Viewed by 4910

Abstract

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. [...] Read more.

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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36 pages, 2126 KiB

Open AccessReview

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

by Shivali Sharma, Albert W. Schulthess, Filippo M. Bassi, Ekaterina D. Badaeva, Kerstin Neumann, Andreas Graner, Hakan Özkan, Peter Werner, Helmut Knüpffer and Benjamin Kilian

Biology 2021, 10(10), 982; https://doi.org/10.3390/biology10100982 - 29 Sep 2021

Cited by 43 | Viewed by 5830

Abstract

Wheat (Triticum sp.) is one of the world’s most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the [...] Read more.

Wheat (Triticum sp.) is one of the world’s most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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46 pages, 8500 KiB

Open AccessReview

Epigenetics for Crop Improvement in Times of Global Change

by Ioanna Kakoulidou, Evangelia V. Avramidou, Miroslav Baránek, Sophie Brunel-Muguet, Sara Farrona, Frank Johannes, Eirini Kaiserli, Michal Lieberman-Lazarovich, Federico Martinelli, Velimir Mladenov, Pilar S. Testillano, Valya Vassileva and Stéphane Maury

Biology 2021, 10(8), 766; https://doi.org/10.3390/biology10080766 - 11 Aug 2021

Cited by 52 | Viewed by 9737

Abstract

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and [...] Read more.

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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16 pages, 1574 KiB

Open AccessReview

Doubled Haploids in Eggplant

by Ricardo Mir, Antonio Calabuig-Serna and Jose M. Seguí-Simarro

Biology 2021, 10(7), 685; https://doi.org/10.3390/biology10070685 - 20 Jul 2021

Cited by 8 | Viewed by 4026

Abstract

Eggplant is a solanaceous crop cultivated worldwide for its edible fruit. Eggplant breeding programs are mainly aimed to the generation of F1 hybrids by crossing two highly homozygous, pure lines, which are traditionally obtained upon several self crossing generations, which is an expensive [...] Read more.

Eggplant is a solanaceous crop cultivated worldwide for its edible fruit. Eggplant breeding programs are mainly aimed to the generation of F1 hybrids by crossing two highly homozygous, pure lines, which are traditionally obtained upon several self crossing generations, which is an expensive and time consuming process. Alternatively, fully homozygous, doubled haploid (DH) individuals can be induced from haploid cells of the germ line in a single generation. Several attempts have been made to develop protocols to produce eggplant DHs principally using anther culture and isolated microspore culture. Eggplant could be considered a moderately recalcitrant species in terms of ability for DH production. Anther culture stands nowadays as the most valuable technology to obtain eggplant DHs. However, the theoretical possibility of having plants regenerated from somatic tissues of the anther walls cannot be ruled out. For this reason, the use of isolated microspores is recommended when possible. This approach still has room for improvement, but it is largely genotype-dependent. In this review, we compile the most relevant advances made in DH production in eggplant, their application to breeding programs, and the future perspectives for the development of other, less genotype-dependent, DH technologies. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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8 pages, 741 KiB

Open AccessOpinion

Designing the Crops for the Future; The CropBooster Program

by Jeremy Harbinson, Martin A. J. Parry, Jess Davies, Norbert Rolland, Francesco Loreto, Ralf Wilhelm, Karin Metzlaff and René Klein Lankhorst

Biology 2021, 10(7), 690; https://doi.org/10.3390/biology10070690 - 20 Jul 2021

Cited by 12 | Viewed by 6110

Abstract

The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation’s Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional [...] Read more.

The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation’s Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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6 pages, 223 KiB

Open AccessBrief Report

Capturing Multiple Disease Resistance in Wheat through Intergeneric Hybridization

by George Fedak, Dawn Chi, Colin Hiebert, Tom Fetch, Brent McCallum, Allen Xue and Wenguang Cao

Biology 2021, 10(7), 631; https://doi.org/10.3390/biology10070631 - 08 Jul 2021

Cited by 1 | Viewed by 1935

Abstract

Derivatives from 4 species from the secondary gene pool of wheat—1 diploid (T. monococcum), 2 tetraploid (T. carthlicum; T. timopheevi), and 1 hexaploid (T. miguschovae)—were screened for resistance to Fusarium head blight, leaf rust, stem rust, [...] Read more.

Derivatives from 4 species from the secondary gene pool of wheat—1 diploid (T. monococcum), 2 tetraploid (T. carthlicum; T. timopheevi), and 1 hexaploid (T. miguschovae)—were screened for resistance to Fusarium head blight, leaf rust, stem rust, and stripe rust. Where screening, genetic studies, and mapping were completed it was shown that all species carried resistance to multiple plant diseases. Some derived lines carried resistance to up to four different diseases. Where mapping was completed, it was shown that different diseases mapped to different chromosomes within any one accession. Full article

(This article belongs to the Special Issue Crop Improvement Now and Beyond)

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