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Open AccessArticle

Durum Wheat Breeding: In the Heat of the Senegal River

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Abdelkarim Filali-Maltouf

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Rodomiro Ortiz

Agriculture 2018, 8(7), 99; https://doi.org/10.3390/agriculture8070099 - 02 Jul 2018

Cited by 11 | Viewed by 4977

Abstract

Global warming may cause +4 °C temperature increases before the end of this century. Heat tolerant bred-germplasm remains the most promising method to ensure farm productivity under this scenario. A global set of 384 durum wheat accessions were exposed to very high temperatures [...] Read more.

Global warming may cause +4 °C temperature increases before the end of this century. Heat tolerant bred-germplasm remains the most promising method to ensure farm productivity under this scenario. A global set of 384 durum wheat accessions were exposed to very high temperatures occurring along the Senegal River at two sites for two years. The goal was to identify germplasm with enhanced tolerance to heat. There was significant variation for all traits. The genetic (G) effect accounted for >15% of the total variation, while the genotype by environment interaction (G × E) reached 25%. A selection index that combines G and a G × E wide adaptation index was used to identify stable high yielding germplasm. Forty-eight accessions had a stable grain yield above the average (2.7 t ha⁻¹), with the three top lines above 3.5 t ha⁻¹. Flowering time, spike fertility and harvest index were the most critical traits for heat tolerance, while 1000-kernel weight and spike density only had environment-specific effects. Testing of six subpopulations for grain yield across heat-prone sites revealed an even distribution among clusters, thus showing the potential of this panel for dissecting heat tolerance via association genetics. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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Open AccessFeature PaperArticle

The Genetic Variability of Floral and Agronomic Characteristics of Newly-Bred Cytoplasmic Male Sterile Rice

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Raafat El-Namaky

Agriculture 2018, 8(5), 68; https://doi.org/10.3390/agriculture8050068 - 11 May 2018

Cited by 5 | Viewed by 4992

Abstract

Male sterility enabled commercialization of heterosis in rice but low seed set remains a constraint on hybrid dissemination. We evaluated 216 F₆ maintainer lines for agronomic and floral characteristics in augmented design and selected 15 maintainer lines, which were testcrossed with IR58025A. [...] Read more.

Male sterility enabled commercialization of heterosis in rice but low seed set remains a constraint on hybrid dissemination. We evaluated 216 F₆ maintainer lines for agronomic and floral characteristics in augmented design and selected 15 maintainer lines, which were testcrossed with IR58025A. Five backcrosses were conducted to transfer cytoplasmic male sterility (CMS) to select maintainer lines. Newly-bred BC_5:6 CMS lines were evaluated for outcrossing rates and agronomic characteristics. There were highly significant differences among 216 F₆ maintainer lines for characteristics whose genotypic variance was higher than environmental variance. The phenotypic coefficient of variation was almost the same as the genotypic coefficient of variation, indicating that most phenotypic variation was due to genetics. There were highly significant differences among CMS lines for number of days to 50% flowering and maturity; stigma exertion; panicle exertion, length and weight; spikelet fertility; tillers per plant; plant height; grains per panicle; grain yield per plant; and 1000-grain weight, but not for pollen and panicle sterility during dry and wet seasons. Three CMS lines (CMS3, CMS12, and CMS14), exhibited high outcrossing rates (56.17%, 51.42% and 48.44%, respectively), which had a highly significant, positive correlation with stigma exertion (0.97), spikelet opening angle (0.82), and panicle exertion (0.95). Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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Open AccessArticle

Identification of Phenotypic Variation and Genetic Diversity in Rice (Oryza sativa L.) Mutants

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Truong Thi Tu Anh

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Tran Dang Khanh

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Tran Dang Dat

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Tran Dang Xuan

Agriculture 2018, 8(2), 30; https://doi.org/10.3390/agriculture8020030 - 24 Feb 2018

Cited by 21 | Viewed by 5939

Abstract

In this study, phenotypic variation and genetic diversity, important factors to decide germplasm for rice breeding, were evaluated among 15 rice mutants attained from the MNU (N-Nitroso-N-methylurea) mutation. The correlation coefficient values among these phenotypic characteristics were calculated. The [...] Read more.

In this study, phenotypic variation and genetic diversity, important factors to decide germplasm for rice breeding, were evaluated among 15 rice mutants attained from the MNU (N-Nitroso-N-methylurea) mutation. The correlation coefficient values among these phenotypic characteristics were calculated. The results showed that full grain number per plant was the most relevant factor contributing to grain yield per plant, and grain length to width ratio was the key parameter affected to amylose content. Furthermore, the genetic variation among mutants was estimated by Simple Sequence Repeat (SSR) markers related to amylose content trait. Fifty-six polymorphism markers covering across eleven rice chromosomes were recorded with an average of 3.02 alleles per locus. The average value of polymorphism information content was 0.47. By using the unweighted pair group method with arithmetic mean (UPGMA) clustering, four clusters were generated with the genetic similarities ranging from 0.52 to 0.91. The variation among groups was 34%, while the variation among individuals within groups was 66%. Findings of this study provided useful genetic background and phenotypic information of collected rice mutants to breed rice cultivars with improved quality. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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Review

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Open AccessReview

Can Parentage Analysis Facilitate Breeding Activities in Root and Tuber Crops?

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Prince Emmanuel Norman

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Asrat Asfaw

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Pangirayi Bernard Tongoona

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Agyemang Danquah

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Eric Yirenkyi Danquah

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David De Koeyer

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Robert Asiedu

Agriculture 2018, 8(7), 95; https://doi.org/10.3390/agriculture8070095 - 27 Jun 2018

Cited by 11 | Viewed by 4840

Abstract

Controlled pollination in root and tuber crops is challenging. Complex ploidy, cross-incompatibility, erratic flowering patterns, outcrossing, etc., limit the efficiency of breeding progress in these crops. Half-sib breeding that involves random pollination among parents is a viable method to harness genetic gain in [...] Read more.

Controlled pollination in root and tuber crops is challenging. Complex ploidy, cross-incompatibility, erratic flowering patterns, outcrossing, etc., limit the efficiency of breeding progress in these crops. Half-sib breeding that involves random pollination among parents is a viable method to harness genetic gain in outcrossing crops that are problematic for performing planned and controlled pollination. The authenticity of resulting progenies from the half-sib breeding is essential to monitor the selection gain in the breeding program. Parentage analysis facilitated by molecular markers is among the available handy tools for crop breeders to maximize genetic gain in a breeding program. It can help to resolve the identity of half-sib progenies and reconstruct the pedigree in the outcrossing crops. This paper reviews the potential benefits of parentage analysis in breeding selected outcrossing root and tuber crops. It assesses how paternity analysis facilitates breeding activities and the ways it improves genetic gain in the root and tuber breeding programs. Conscious use of complementary techniques in the root and tuber breeding programs can increase the selection gain by reducing the long breeding cycle and cost, as well as reliable exploitation of the heritable variation in the desired direction. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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Open AccessReview

Genomics-Assisted Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB)

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Ranjana Bhattacharjee

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Allan Brown

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Edward Carey

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Morag Elizabeth Ferguson

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Dorcus Gemenet

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Hanele Lindqvist-Kreuze

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Agriculture 2018, 8(7), 89; https://doi.org/10.3390/agriculture8070089 - 22 Jun 2018

Cited by 14 | Viewed by 6585

Abstract

Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB) targets highly diverse biotic and abiotic constraints, whilst meeting complex end-user quality preferences to improve livelihoods of beneficiaries in developing countries. Achieving breeding targets and increasing the rate of genetic gains [...] Read more.

Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB) targets highly diverse biotic and abiotic constraints, whilst meeting complex end-user quality preferences to improve livelihoods of beneficiaries in developing countries. Achieving breeding targets and increasing the rate of genetic gains for these vegetatively propagated crops, with long breeding cycles, and genomes with high heterozygosity and different ploidy levels, is challenging. Cheaper sequencing opens possibilities to apply genomics tools for complex traits, such as yield, climate resilience, and quality traits. Therefore, across the RTB program, genomic resources and approaches, including sequenced draft genomes, SNP discovery, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS), are at different stages of development and implementation. For some crops, marker-assisted selection (MAS) is being implemented, and GS has passed the proof-of-concept stage. Depending on the traits being selected for using prediction models, breeding schemes will most likely have to incorporate both GS and phenotyping for other traits into the workflows leading to varietal development. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

Open AccessFeature PaperReview

Chitinases—Potential Candidates for Enhanced Plant Resistance towards Fungal Pathogens

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Agriculture 2018, 8(7), 88; https://doi.org/10.3390/agriculture8070088 - 22 Jun 2018

Cited by 92 | Viewed by 10581

Abstract

Crop cultivation is crucial for the existence of human beings, as it fulfills our nutritional requirements. Crops and other plants are always at a high risk of being attacked by phytopathogens, especially pathogenic fungi. Although plants have a well-developed defense system, it can [...] Read more.

Crop cultivation is crucial for the existence of human beings, as it fulfills our nutritional requirements. Crops and other plants are always at a high risk of being attacked by phytopathogens, especially pathogenic fungi. Although plants have a well-developed defense system, it can be compromised during pathogen attack. Chitinases can enhance the plant’s defense system as they act on chitin, a major component of the cell wall of pathogenic fungi, and render the fungi inactive without any negative impact on the plants. Along with strengthening plant defense mechanisms, chitinases also improve plant growth and yield. Chitinases in combination with recombinant technology can be a promising tool for improving plant resistance to fungal diseases. The applicability of chitinase-derived oligomeric products of chitin further augment chitinase prospecting to enhance plant defense and growth. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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Open AccessFeature PaperReview

Genetic Engineering of Energy Crops to Reduce Recalcitrance and Enhance Biomass Digestibility

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Vivekanand Vivekanand

Agriculture 2018, 8(6), 76; https://doi.org/10.3390/agriculture8060076 - 02 Jun 2018

Cited by 17 | Viewed by 6220

Abstract

Bioenergy, biofuels, and a range of valuable chemicals may be extracted from the abundantly available lignocellulosic biomass. To reduce the recalcitrance imposed by the complex cell wall structure, genetic engineering has been proposed over the years as a suitable solution to modify the [...] Read more.

Bioenergy, biofuels, and a range of valuable chemicals may be extracted from the abundantly available lignocellulosic biomass. To reduce the recalcitrance imposed by the complex cell wall structure, genetic engineering has been proposed over the years as a suitable solution to modify the genes, thereby, controlling the overall phenotypic expression. The present review provides a brief description of the plant cell wall structure and its compositional array i.e., lignin, cellulose, hemicellulose, wall proteins, and pectin, along with their effect on biomass digestibility. Also, this review discusses the potential to increase biomass by gene modification. Furthermore, the review highlights the potential genes associated with the regulation of cell wall structure, which can be targeted for achieving energy crops with desired phenotypes. These genetic approaches provide a robust and assured method to bring about the desired modifications in cell wall structure, composition, and characteristics. Ultimately, these genetic modifications pave the way for achieving enhanced biomass yield and enzymatic digestibility of energy crops, which is crucial for maximizing the outcomes of energy crop breeding and biorefinery applications. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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Open AccessReview

Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline

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Haifei Hu

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Armin Scheben

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David Edwards

Agriculture 2018, 8(6), 75; https://doi.org/10.3390/agriculture8060075 - 31 May 2018

Cited by 49 | Viewed by 17058

Abstract

With the global human population growing rapidly, agricultural production must increase to meet crop demand. Improving crops through breeding is a sustainable approach to increase yield and yield stability without intensifying the use of fertilisers and pesticides. Current advances in genomics and bioinformatics [...] Read more.

With the global human population growing rapidly, agricultural production must increase to meet crop demand. Improving crops through breeding is a sustainable approach to increase yield and yield stability without intensifying the use of fertilisers and pesticides. Current advances in genomics and bioinformatics provide opportunities for accelerating crop improvement. The rise of third generation sequencing technologies is helping overcome challenges in plant genome assembly caused by polyploidy and frequent repetitive elements. As a result, high-quality crop reference genomes are increasingly available, benefitting downstream analyses such as variant calling and association mapping that identify breeding targets in the genome. Machine learning also helps identify genomic regions of agronomic value by facilitating functional annotation of genomes and enabling real-time high-throughput phenotyping of agronomic traits in the glasshouse and in the field. Furthermore, crop databases that integrate the growing volume of genotype and phenotype data provide a valuable resource for breeders and an opportunity for data mining approaches to uncover novel trait-associated candidate genes. As knowledge of crop genetics expands, genomic selection and genome editing hold promise for breeding diseases-resistant and stress-tolerant crops with high yields. Full article

(This article belongs to the Special Issue Plant Breeding in Agriculture)

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