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5 pages, 202 KiB

Open AccessEditorial

Molecular Marker Technology for Crop Improvement

by Jose Miguel Soriano

Agronomy 2020, 10(10), 1462; https://doi.org/10.3390/agronomy10101462 - 24 Sep 2020

Cited by 7 | Viewed by 4709

Abstract

Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, [...] Read more.

Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, but the results have been costly and time-consuming, due to the small number of markers that could be tested simultaneously. Recent advances in molecular marker technologies such as the development of high-throughput genotyping platforms, genotyping by sequencing, and the release of the genome sequences of major crop plants open new possibilities for advancing crop improvement. This Special Issue collects sixteen research studies, including the application of molecular markers in eleven crop species, from the generation of linkage maps and diversity studies to the application of marker-assisted selection and genomic prediction. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

Research

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29 pages, 2813 KiB

Open AccessArticle

High Resolution Melting and Insertion Site-Based Polymorphism Markers for Wheat Variability Analysis and Candidate Genes Selection at Drought and Heat MQTL Loci

by Rosa Mérida-García, Sergio Gálvez, Etienne Paux, Gabriel Dorado, Laura Pascual, Patricia Giraldo and Pilar Hernandez

Agronomy 2020, 10(9), 1294; https://doi.org/10.3390/agronomy10091294 - 01 Sep 2020

Cited by 5 | Viewed by 3249

Abstract

The practical use of molecular markers is facilitated by cost-effective detection techniques. In this work, wheat insertion site-based polymorphisms (ISBP) markers were set up for genotyping using high-resolution melting analysis (HRM). Polymorphic HRM-ISBP assays were developed for wheat chromosomes 4A and 3B and [...] Read more.

The practical use of molecular markers is facilitated by cost-effective detection techniques. In this work, wheat insertion site-based polymorphisms (ISBP) markers were set up for genotyping using high-resolution melting analysis (HRM). Polymorphic HRM-ISBP assays were developed for wheat chromosomes 4A and 3B and used for wheat variability assessment. The marker sequences were mapped against the wheat genome reference sequence, targeting interesting genes. Those genes were located within or in proximity to previously described quantitative trait loci (QTL) or meta-quantitative trait loci (MQTL) for drought and heat stress tolerance, and also yield and yield related traits. Eighteen of the markers used tagged drought related genes and, interestingly, eight of the genes were differentially expressed under different abiotic stress conditions. These results confirmed HRM as a cost-effective and efficient tool for wheat breeding programs. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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25 pages, 3483 KiB

Open AccessArticle

Cost-Effective and Time-Efficient Molecular Assisted Selection for PPV Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

by Ángela Polo-Oltra, Carlos Romero, Inmaculada López, María Luisa Badenes and Elena Zuriaga

Agronomy 2020, 10(9), 1292; https://doi.org/10.3390/agronomy10091292 - 31 Aug 2020

Cited by 10 | Viewed by 4097

Abstract

Plum pox virus (PPV) is the most important limiting factor for apricot (Prunus armeniaca L.) production worldwide, and development of resistant cultivars has been proven to be the best solution in the long-term. However, just like in other woody species, apricot breeding [...] Read more.

Plum pox virus (PPV) is the most important limiting factor for apricot (Prunus armeniaca L.) production worldwide, and development of resistant cultivars has been proven to be the best solution in the long-term. However, just like in other woody species, apricot breeding is highly time and space demanding, and this is particularly true for PPV resistance phenotyping. Therefore, marker-assisted selection (MAS) may be very helpful to speed up breeding programs. Tightly linked ParPMC1 and ParPMC2, meprin and TRAF-C homology (MATH)-domain-containing genes have been proposed as host susceptibility genes required for PPV infection. Contribution of additional genes to PPV resistance cannot be discarded, but all available studies undoubtedly show a strong correlation between ParPMC2-resistant alleles (ParPMC2res) and PPV resistance. The ParPMC2res allele was shown to carry a 5-bp deletion (ParPMC2-del) within the second exon that has been characterized as a molecular marker suitable for MAS (PMC2). Based on this finding, we propose here a method for PPV resistance selection in apricot by combining high-throughput DNA extraction of 384 samples in 2 working days and the allele-specific genotyping of PMC2 on agarose gel. Moreover, the PMC2 genotype has been determined by PCR or by using whole-genome sequences (WGS) in 175 apricot accessions. These results were complemented with phenotypic and/or genotypic data available in the literature to reach a total of 325 apricot accessions. As a whole, we conclude that this is a time-efficient, cost-effective and straightforward method for PPV resistance screening that can be highly useful for apricot breeding programs. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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18 pages, 1752 KiB

Open AccessArticle

QTL Mapping for Seedling and Adult Plant Resistance to Leaf and Stem Rusts in Pamyati Azieva × Paragon Mapping Population of Bread Wheat

by Yuliya Genievskaya, Saule Abugalieva, Aralbek Rsaliyev, Gulbahar Yskakova and Yerlan Turuspekov

Agronomy 2020, 10(9), 1285; https://doi.org/10.3390/agronomy10091285 - 30 Aug 2020

Cited by 9 | Viewed by 2880

Abstract

Leaf rust (LR) and stem rust (SR) pose serious challenges to wheat production in Kazakhstan. In recent years, the susceptibility of local wheat cultivars has substantially decreased grain yield and quality. Therefore, local breeding projects must be adjusted toward the improvement of LR [...] Read more.

Leaf rust (LR) and stem rust (SR) pose serious challenges to wheat production in Kazakhstan. In recent years, the susceptibility of local wheat cultivars has substantially decreased grain yield and quality. Therefore, local breeding projects must be adjusted toward the improvement of LR and SR disease resistances, including genetic approaches. In this study, a spring wheat segregating population of Pamyati Azieva (PA) × Paragon (Par), consisting of 98 recombinant inbred lines (RILs), was analyzed for the resistance to LR and SR at the seedling and adult plant-growth stages. In total, 24 quantitative trait loci (QTLs) for resistance to rust diseases at the seedling and adult plant stages were identified, including 11 QTLs for LR and 13 QTLs for SR resistances. Fourteen QTLs were in similar locations to QTLs and major genes detected in previous linkage mapping and genome-wide association studies. The remaining 10 QTLs are potentially new genetic factors for LR and SR resistance in wheat. Overall, the QTLs revealed in this study may play an important role in the improvement of wheat resistance to LR and SR per the marker-assisted selection approach. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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15 pages, 2347 KiB

Open AccessArticle

Multi-Trait Regressor Stacking Increased Genomic Prediction Accuracy of Sorghum Grain Composition

by Sirjan Sapkota, J. Lucas Boatwright, Kathleen Jordan, Richard Boyles and Stephen Kresovich

Agronomy 2020, 10(9), 1221; https://doi.org/10.3390/agronomy10091221 - 19 Aug 2020

Cited by 16 | Viewed by 2976

Abstract

Genomic prediction has enabled plant breeders to estimate breeding values of unobserved genotypes and environments. The use of genomic prediction will be extremely valuable for compositional traits for which phenotyping is labor-intensive and destructive for most accurate results. We studied the potential of [...] Read more.

Genomic prediction has enabled plant breeders to estimate breeding values of unobserved genotypes and environments. The use of genomic prediction will be extremely valuable for compositional traits for which phenotyping is labor-intensive and destructive for most accurate results. We studied the potential of Bayesian multi-output regressor stacking (BMORS) model in improving prediction performance over single trait single environment (STSE) models using a grain sorghum diversity panel (GSDP) and a biparental recombinant inbred lines (RILs) population. A total of five highly correlated grain composition traits—amylose, fat, gross energy, protein and starch, with genomic heritability ranging from 0.24 to 0.59 in the GSDP and 0.69 to 0.83 in the RILs were studied. Average prediction accuracies from the STSE model were within a range of 0.4 to 0.6 for all traits across both populations except amylose (0.25) in the GSDP. Prediction accuracy for BMORS increased by 41% and 32% on average over STSE in the GSDP and RILs, respectively. Prediction of whole environments by training with remaining environments in BMORS resulted in moderate to high prediction accuracy. Our results show regression stacking methods such as BMORS have potential to accurately predict unobserved individuals and environments, and implementation of such models can accelerate genetic gain. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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11 pages, 4797 KiB

Open AccessArticle

Molecular Assisted Selection for Pollination-Constant and Non-Astringent Type without Male Flowers in Spanish Germplasm for Persimmon Breeding

by Manuel Blasco, Francisco Gil-Muñoz, María del Mar Naval and María Luisa Badenes

Agronomy 2020, 10(8), 1172; https://doi.org/10.3390/agronomy10081172 - 11 Aug 2020

Cited by 4 | Viewed by 2982

Abstract

Persimmon (Diospyros kaki Thunb) species is a hexaploid genotype that has a morphologically polygamous gyonodioecious sexual system. D. kaki bears unisexual flowers. The presence of male flowers resulted in the presence of seeds in the varieties. The fruits of persimmon are classified [...] Read more.

Persimmon (Diospyros kaki Thunb) species is a hexaploid genotype that has a morphologically polygamous gyonodioecious sexual system. D. kaki bears unisexual flowers. The presence of male flowers resulted in the presence of seeds in the varieties. The fruits of persimmon are classified according to their astringency and the pollination events that produced seeds and modify the levels of astringency in the fruit. The presence of seeds in astringent varieties as pollination variant astringent (PVA), pollination variant non-astringent (PVNA) and pollination constant astringent (PCA) resulted in fruits not marketable. Molecular markers that allow selection of the varieties according to the type of flowers at the plantlet stage would allow selection of seedless varieties. In this study, a marker developed in D. lotus by bulk segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) markers, named DlSx-AF4, has been validated in a germplasm collection of persimmon, results obtained agree with the phenotype data. A second important trait in persimmon is the presence of astringency in ripened fruits. Fruits non-astringent at the ripen stage named pollination constant non-astringent (PCNA) are the objective of many breeding programs as they do not need removal of the astringency by a postharvest treatment. Astringency in the hexaploid persimmon is a dominant trait. The presence of at least one astringent allele confers astringency to the fruit. In this paper we checked the marker developed linked to the AST gene. Our goal has been to validate both markers in germplasm from different origins and to test the usefulness in a breeding program. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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18 pages, 931 KiB

Open AccessArticle

Identification of QTLs Controlling Resistance/Tolerance to Striga hermonthica in an Extra-Early Maturing Yellow Maize Population

by Baffour Badu-Apraku, Samuel Adewale, Agre Paterne, Melaku Gedil and Robert Asiedu

Agronomy 2020, 10(8), 1168; https://doi.org/10.3390/agronomy10081168 - 10 Aug 2020

Cited by 23 | Viewed by 3365

Abstract

Striga hermonthica parasitism is a major constraint to maize production in sub-Saharan Africa with yield losses reaching 100% under severe infestation. The application of marker-assisted selection is highly promising for accelerating breeding for Striga resistance/tolerance in maize but requires the identification of quantitative [...] Read more.

Striga hermonthica parasitism is a major constraint to maize production in sub-Saharan Africa with yield losses reaching 100% under severe infestation. The application of marker-assisted selection is highly promising for accelerating breeding for Striga resistance/tolerance in maize but requires the identification of quantitative trait loci (QTLs) linked to Striga resistance/tolerance traits. In the present study, 194 F_2:3 families of TZEEI 79 × TZdEEI 11 were screened at two Striga-endemic locations in Nigeria, to identify QTLs associated with S. hermonthica resistance/tolerance and underlying putative candidate genes. A genetic map was constructed using 1139 filtered DArTseq markers distributed across the 10 maize chromosomes, covering 2016 cM, with mean genetic distance of 1.70 cM. Twelve minor and major QTLs were identified for four Striga resistance/tolerance adaptive traits, explaining 19.4%, 34.9%, 14.2% and 3.2% of observed phenotypic variation for grain yield, ears per plant, Striga damage and emerged Striga plants, respectively. The QTLs were found to be linked to candidate genes which may be associated with plant defense mechanisms in S. hermonthica infested environments. The results of this study provide insights into the genetic architecture of S. hermonthica resistance/tolerance indicator traits which could be employed for marker-assisted selection to accelerate efficient transfer host plant resistance genes to susceptible genotypes. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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17 pages, 1289 KiB

Open AccessArticle

Improvement of a RD6 Rice Variety for Blast Resistance and Salt Tolerance through Marker-Assisted Backcrossing

by Korachan Thanasilungura, Sukanya Kranto, Tidarat Monkham, Sompong Chankaew and Jirawat Sanitchon

Agronomy 2020, 10(8), 1118; https://doi.org/10.3390/agronomy10081118 - 01 Aug 2020

Cited by 12 | Viewed by 3841

Abstract

RD6 is one of the most favorable glutinous rice varieties consumed throughout the north and northeast of Thailand because of its aroma and softness. However, blast disease and salt stress cause decreases in both yield quantity and quality during cultivation. Here, gene pyramiding [...] Read more.

RD6 is one of the most favorable glutinous rice varieties consumed throughout the north and northeast of Thailand because of its aroma and softness. However, blast disease and salt stress cause decreases in both yield quantity and quality during cultivation. Here, gene pyramiding via marker-assisted backcrossing (MAB) using combined blast resistance QTLs (qBl 1, 2, 11, and 12) and Saltol QTL was employed in solving the problem. To pursue our goal, the RD6 introgression line (RGD07005-12-165-1), containing four blast-resistant QTLs, were crossed with the Pokkali salt tolerant variety. Blast resistance evaluation was thoroughly carried out in the fields, from BC₂F_2:3 to BC₄F₄, using the upland short-row and natural field infection methods. Additionally, salt tolerance was validated in both greenhouse and field conditions. We found that the RD6 “BC₄F₄ 132-12-61” resulting from our breeding programme successfully resisted blast disease and tolerated salt stress, while it maintained the desirable agronomic traits of the original RD6 variety. This finding may provide a new improved rice variety to overcome blast disease and salt stress in Northeast Thailand. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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19 pages, 3027 KiB

Open AccessEditor’s ChoiceArticle

Exploring the Genetic Architecture of Root-Related Traits in Mediterranean Bread Wheat Landraces by Genome-Wide Association Analysis

by Rubén Rufo, Silvio Salvi, Conxita Royo and Jose Miguel Soriano

Agronomy 2020, 10(5), 613; https://doi.org/10.3390/agronomy10050613 - 25 Apr 2020

Cited by 21 | Viewed by 3829

Abstract

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers [...] Read more.

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers linked to RSA traits is of special interest to the breeding community. The reported correlation between the RSA of seedlings and adult plants simplifies its assessment. Methods: In this study, a panel of 170 bread wheat landraces from 24 Mediterranean countries was used to identify molecular markers associated with the seminal RSA and related traits: seminal root angle, total root number, root dry weight, seed weight and shoot length, and grain yield (GY). Results: A genome-wide association study identified 135 marker-trait associations explaining 6% to 15% of the phenotypic variances for root related traits and 112 for GY. Fifteen QTL hotspots were identified as the most important for controlling root trait variation and were shown to include 31 candidate genes related to RSA traits, seed size, root development, and abiotic stress tolerance (mainly drought). Co-location for root related traits and GY was found in 17 genome regions. In addition, only four out of the fifteen QTL hotspots were reported previously. Conclusions: The variability found in the Mediterranean wheat landraces is a valuable source of root traits to introgress into adapted phenotypes through marker-assisted breeding. The study reveals new loci affecting root development in wheat. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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23 pages, 1445 KiB

Open AccessArticle

Mapping Agronomic and Quality Traits in Elite Durum Wheat Lines under Differing Water Regimes

by Rosa Mérida-García, Alison R. Bentley, Sergio Gálvez, Gabriel Dorado, Ignacio Solís, Karim Ammar and Pilar Hernandez

Agronomy 2020, 10(1), 144; https://doi.org/10.3390/agronomy10010144 - 19 Jan 2020

Cited by 8 | Viewed by 5059

Abstract

Final grain production and quality in durum wheat are affected by biotic and abiotic stresses. The association mapping (AM) approach is useful for dissecting the genetic control of quantitative traits, with the aim of increasing final wheat production under stress conditions. In this [...] Read more.

Final grain production and quality in durum wheat are affected by biotic and abiotic stresses. The association mapping (AM) approach is useful for dissecting the genetic control of quantitative traits, with the aim of increasing final wheat production under stress conditions. In this study, we used AM analyses to detect quantitative trait loci (QTL) underlying agronomic and quality traits in a collection of 294 elite durum wheat lines from CIMMYT (International Maize and Wheat Improvement Center), grown under different water regimes over four growing seasons. Thirty-seven significant marker-trait associations (MTAs) were detected for sedimentation volume (SV) and thousand kernel weight (TKW), located on chromosomes 1B and 2A, respectively. The QTL loci found were then confirmed with several AM analyses, which revealed 12 sedimentation index (SDS) MTAs and two additional loci for SV (4A) and yellow rust (1B). A candidate gene analysis of the identified genomic regions detected a cluster of 25 genes encoding blue copper proteins in chromosome 1B, with homoeologs in the two durum wheat subgenomes, and an ubiquinone biosynthesis O-methyltransferase gene. On chromosome 2A, several genes related to photosynthetic processes and metabolic pathways were found in proximity to the markers associated with TKW. These results are of potential use for subsequent application in marker-assisted durum wheat-breeding programs. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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14 pages, 11359 KiB

Open AccessArticle

An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology

by Xiaoxia Yu, Mingfei Zhang, Zhuo Yu, Dongsheng Yang, Jingwei Li, Guofang Wu and Jiaqi Li

Agronomy 2020, 10(1), 114; https://doi.org/10.3390/agronomy10010114 - 13 Jan 2020

Cited by 9 | Viewed by 3285

Abstract

Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to [...] Read more.

Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F₁ individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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13 pages, 705 KiB

Open AccessArticle

Identification and Verification of Quantitative Trait Loci Affecting Milling Yield of Rice

by Hui Zhang, Yu-Jun Zhu, An-Dong Zhu, Ye-Yang Fan, Ting-Xu Huang, Jian-Fu Zhang, Hua-An Xie and Jie-Yun Zhuang

Agronomy 2020, 10(1), 75; https://doi.org/10.3390/agronomy10010075 - 05 Jan 2020

Cited by 12 | Viewed by 2811

Abstract

Rice is generally consumed in the form of milled rice. The yield of total milled rice and head mill rice is affected by both the paddy rice yield and milling efficiency. In this study, three recombinant inbred line (RIL) populations and one F [...] Read more.

Rice is generally consumed in the form of milled rice. The yield of total milled rice and head mill rice is affected by both the paddy rice yield and milling efficiency. In this study, three recombinant inbred line (RIL) populations and one F_4:5 population derived from a residual heterozygous (RH) plant were used to determine quantitative trait loci (QTLs) affecting milling yield of rice. Seven traits were analyzed, including recovery of brown rice (BR), milled rice (MR) and head rice (HR); grain yield (GY); and the yield of brown rice (BRY), milled rice (MRY) and head rice (HRY). A total of 77 QTLs distributed on 35 regions was detected in the three RIL populations. Four regions, where qBR5, qBR7, qBR10, and qBR12 were located, were validated in the RH-derived F_4:5 population. In the three RIL populations, all the 11 QTLs for GY detected were accompanied with QTLs for two or all the three milling yield traits. Not only the allele direction for milling yield traits was unchanged, but also the effects were consistent with GY. In the RH-derived F_4:5 population, regions controlling GY also affected all three milling yield traits. Results indicated that variations of BRY and MRY were mainly ascribed to GY, but HRY was determined by both GY and HR. Results also showed that the regions covering GW5–Chalk5 and Wx loci had major effects on milling quality and milling yield of rice. These two regions, which have been known to affect multiple traits determining grain quality and yield of rice, provide good candidates for milled yield improvement. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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10 pages, 746 KiB

Open AccessCommunication

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Maize with Network-Assisted Gene Prioritization

by Carlos Maldonado, Freddy Mora, Filipe Augusto Bengosi Bertagna, Maurício Carlos Kuki and Carlos Alberto Scapim

Agronomy 2019, 9(11), 725; https://doi.org/10.3390/agronomy9110725 - 07 Nov 2019

Cited by 14 | Viewed by 3899

Abstract

Maize (Zea mays L.) is one of the most crucial crops for global food security worldwide. For this reason, many efforts have been undertaken to address the efficient utilization of germplasm collections. In this study, 322 inbred lines were used to link [...] Read more.

Maize (Zea mays L.) is one of the most crucial crops for global food security worldwide. For this reason, many efforts have been undertaken to address the efficient utilization of germplasm collections. In this study, 322 inbred lines were used to link genotypic variations (53,403 haplotype blocks (HBs) and 290,973 single nucleotide polymorphisms (SNPs)) to corresponding differences in flowering-related traits in two locations in Southern Brazil. Additionally, network-assisted gene prioritization (NAGP) was applied in order to better understand the genetic basis of flowering-related traits in tropical maize. According to the results, the linkage disequilibrium (LD) decayed rapidly within 3 kb, with a cut-off value of r² = 0.11. Total values of 45 and 44 marker-trait associations (SNPs and HBs, respectively) were identified. Another important finding was the identification of HBs, explaining more than 10% of the total variation. NAGP identified 44, 22, and 34 genes that are related to female/male flowering time and anthesis-silking interval, respectively. The co-functional network approach identified four genes directly related to female flowering time (p < 0.0001): GRMZM2G013398, GRMZM2G021614, GRMZM2G152689, and GRMZM2G117057. NAGP provided new insights into the genetic architecture and mechanisms underlying flowering-related traits in tropical maize. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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13 pages, 1942 KiB

Open AccessArticle

Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid Biosynthesis Genes

by Vadim G. Lebedev, Natalya M. Subbotina, Oleg P. Maluchenko, Konstantin V. Krutovsky and Konstantin A. Shestibratov

Agronomy 2019, 9(9), 518; https://doi.org/10.3390/agronomy9090518 - 06 Sep 2019

Cited by 11 | Viewed by 3017

Abstract

Raspberry is a valuable berry crop containing a large amount of antioxidants that correlates with the color of the berries. We evaluated the genetic diversity of differently colored raspberry cultivars by the microsatellite markers developed using the flavonoid biosynthesis structural and regulatory genes. [...] Read more.

Raspberry is a valuable berry crop containing a large amount of antioxidants that correlates with the color of the berries. We evaluated the genetic diversity of differently colored raspberry cultivars by the microsatellite markers developed using the flavonoid biosynthesis structural and regulatory genes. Among nine tested markers, seven were polymorphic. In total, 26 alleles were found at seven loci in 19 red (Rubus idaeus L.) and two black (R. occidentalis L.) raspberry cultivars. The most polymorphic marker was RiMY01 located in the MYB10 transcription factor intron region. Its polymorphic information content (PIC) equalled 0.82. The RiG001 marker that previously failed to amplify in blackberry also failed in black raspberry. The raspberry cultivar clustering in the UPGMA dendrogram was unrelated to geographical and genetic origin, but significantly correlated with the color of berries. The black raspberry cultivars had a higher homozygosity and clustered separately from other cultivars, while at the same time they differed from each other. In addition, some of the raspberry cultivars with a yellow-orange color of berries formed a separate cluster. This suggests that there may be not a single genetic mechanism for the formation of yellow-orange berries. The data obtained can be used prospectively in future breeding programs to improve the nutritional qualities of raspberry fruits. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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18 pages, 4722 KiB

Open AccessArticle

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

by Yu Ge, Xiaoping Zang, Lin Tan, Jiashui Wang, Yuanzheng Liu, Yanxia Li, Nan Wang, Di Chen, Rulin Zhan and Weihong Ma

Agronomy 2019, 9(9), 512; https://doi.org/10.3390/agronomy9090512 - 05 Sep 2019

Cited by 6 | Viewed by 2520

Abstract

Avocado (Persea americana Mill.) is an important fruit crop commercially grown in tropical and subtropical regions. Despite the importance of avocado, there is relatively little available genomic information regarding this fruit species. In this study, we functionally annotated the full-length avocado transcriptome [...] Read more.

Avocado (Persea americana Mill.) is an important fruit crop commercially grown in tropical and subtropical regions. Despite the importance of avocado, there is relatively little available genomic information regarding this fruit species. In this study, we functionally annotated the full-length avocado transcriptome sequence based on single-molecule real-time sequencing technology, and predicted the coding sequences (CDSs), transcription factors (TFs), and long non-coding RNA (lncRNA) sequences. Moreover, 76,777 simple sequence repeat (SSR) loci detected among the 42,096 SSR-containing transcript sequences were used to develop 149,733 expressed sequence tag (EST)-SSR markers. A subset of 100 EST-SSR markers was randomly chosen for an analysis that detected 15 polymorphicEST-SSR markers, with an average polymorphism information content of 0.45. These 15markers were able to clearly and effectively characterize46 avocado accessions based on geographical origin. In summary, our study is the first to generate a full-length transcriptome sequence and develop and analyze a set of EST-SSR markers in avocado. The application of third-generation sequencing techniques for developing SSR markers is a potentially powerful tool for genetic studies. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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16 pages, 1810 KiB

Open AccessArticle

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

by Jiantao Wu, Qinnan Wang, Jing Xie, Yong-Bao Pan, Feng Zhou, Yuqiang Guo, Hailong Chang, Huanying Xu, Wei Zhang, Chuiming Zhang and Yongsheng Qiu

Agronomy 2019, 9(8), 449; https://doi.org/10.3390/agronomy9080449 - 14 Aug 2019

Cited by 22 | Viewed by 4482

Abstract

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In [...] Read more.

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s). Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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17 pages, 2118 KiB

Open AccessArticle

Genetic Dissection of the Seminal Root System Architecture in Mediterranean Durum Wheat Landraces by Genome-Wide Association Study

by Martina Roselló, Conxita Royo, Miguel Sanchez-Garcia and Jose Miguel Soriano

Agronomy 2019, 9(7), 364; https://doi.org/10.3390/agronomy9070364 - 09 Jul 2019

Cited by 26 | Viewed by 4592

Abstract

Roots are crucial for adaptation to drought stress. However, phenotyping root systems is a difficult and time-consuming task due to the special feature of the traits in the process of being analyzed. Correlations between root system architecture (RSA) at the early stages of [...] Read more.

Roots are crucial for adaptation to drought stress. However, phenotyping root systems is a difficult and time-consuming task due to the special feature of the traits in the process of being analyzed. Correlations between root system architecture (RSA) at the early stages of development and in adult plants have been reported. In this study, the seminal RSA was analysed on a collection of 160 durum wheat landraces from 21 Mediterranean countries and 18 modern cultivars. The landraces showed large variability in RSA, and differences in root traits were found between previously identified genetic subpopulations. Landraces from the eastern Mediterranean region, which is the driest and warmest within the Mediterranean Basin, showed the largest seminal root size in terms of root length, surface, and volume and the widest root angle, whereas landraces from eastern Balkan countries showed the lowest values. Correlations were found between RSA and yield-related traits in a very dry environment. The identification of molecular markers linked to the traits of interest detected 233 marker-trait associations for 10 RSA traits and grouped them in 82 genome regions named marker-train association quantitative trait loci (MTA-QTLs). Our results support the use of ancient local germplasm to widen the genetic background for root traits in breeding programs. Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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1 pages, 199 KiB

Open AccessErratum

Erratum: Polo-Oltra et al. Cost-Effective and Time-Efficient Molecular Assisted Selection for PPV Resistance in Apricot Based on ParPMC2 Allele-Specific PCR. Agronomy 2020, 10, 1292

by Ángela Polo-Oltra, Carlos Romero, Inmaculada López, María Luisa Badenes and Elena Zuriaga

Agronomy 2022, 12(3), 561; https://doi.org/10.3390/agronomy12030561 - 24 Feb 2022

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Abstract

The authors would like to make the following correction to the published paper [...] Full article

(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)

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