Legume Genomics and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 February 2022) | Viewed by 11627

Special Issue Editors

International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol 1108-2010, Lebanon
Interests: legume; breeding; screening for biotic and abiotic stresses; genetic studies; disease resistance; herbicide resistance; genetic gain assessment; genomic assisted breeding; speed breeding; efficient breeding tools and techniques; genotype X environment interaction
Special Issues, Collections and Topics in MDPI journals
Dr. Dil Thavarajah
E-Mail Website1 Website2
Guest Editor
Plant and Environmental Sciences, 270 Poole Agricultural Center, Clemson University, Clemson, SC 29634, USA
Interests: nutritional breeding and biofortification

Special Issue Information

Dear Colleagues,

Legumes are key crops that contribute to sustainable agriculture through their ability to fix atmospheric nitrogen and improve soil structure. In developing countries, they contribute to food and nutritional security through diversified food systems. However, many legume crops remain underutilized due to policy issues that favor cereals over legumes. Legumes are also affected by diverse biotic (diseases, parasitic weeds, and insects) and abiotic stresses (heat, frost, drought, salinity, soil acidity, and nutrient deficiency). Conventional breeding approaches have resulted in significant genetic improvement in legume crops and improved cultivars have been developed for cultivation in different agro-ecologies. However, the genetic gains in major legume crops grown in developing countries remain below the desired rate to close demand–supply gaps. Significant research and development efforts have been undertaken in the past decade concerning important legumes at advanced research Institutes and in the CGIAR centers. These efforts have led to the development of valuable genomic resources and genomic tools, such as draft genome sequencing, resequencing data, large-scale genome-wide markers, dense genetic maps, quantitative trait loci (QTLs), and diagnostic markers. These tools are essential for the modernization of breeding programs and accelerate the breeding cycle, which can increase genetic gains when integrated with the speed breeding approach. This Special Issue will gather innovative papers on genomic research in different legume crops.

Dr. Fouad S. Maalouf
Dr. Dil Thavarajah
Guest Editors

Manuscript Submission Information

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Keywords

  • Genomics in legumes
  • Genetics
  • Molecular breeding and marker-assisted selection/breeding
  • QTL analysis
  • Genomic-assisted breeding
  • Biotic and abiotic stresses
  • Genetic gains
  • Genetic resources and Germplasm enhancement
  • Modern Breeding methods
  • G x E interaction
  • Speed breeding

Published Papers (5 papers)

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Research

17 pages, 2075 KiB  
Article
DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes
Plants 2022, 11(7), 947; https://doi.org/10.3390/plants11070947 - 31 Mar 2022
Cited by 3 | Viewed by 1797
Abstract
Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as [...] Read more.
Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as DNA barcoding, that can enable the effective authentication and identification of species in the genus. In this study, we analysed the chloroplast trnL and rpoC1, as well as the nuclear ITS2 DNA barcoding regions, to identify 71 Vicia specimens of Eurasian descent. Both the trnL and ITS2 regions were highly effective in discriminating the analysed taxa, while the more conserved rpoC1 region could not identify all of the selected species due to high sequence conservation or non-annotated or absent rpoC1 species sequences in GenBank. A dendrographic representation of the generated trnL data showed sufficient clustering for most of the analysed taxa, although some topological discrepancies were observed. ITS2 and rpoC1 reconstructions were also used for resolving the topological discrepancies observed in the trnL tree. Our analysis suggests that a combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus, while single-locus analyses do not provide the necessary resolution. Full article
(This article belongs to the Special Issue Legume Genomics and Breeding)
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23 pages, 3403 KiB  
Article
Stability, the Last Frontier: Forage Yield Dynamics of Peas under Two Cultivation Systems
Plants 2022, 11(7), 892; https://doi.org/10.3390/plants11070892 - 27 Mar 2022
Cited by 4 | Viewed by 1629
Abstract
The stability of performance may be proved to be the last frontier for adopting certain genotypes in various cultivation systems and environments. The main objective of the present study was to analyze the forage yield stability performance of seven pea (Pisum sativum [...] Read more.
The stability of performance may be proved to be the last frontier for adopting certain genotypes in various cultivation systems and environments. The main objective of the present study was to analyze the forage yield stability performance of seven pea (Pisum sativum L.) genotypes based on various stability indices. The genotype behavior was studied based on the yield of peas under both conventional and low-input cultivation systems. Five cultivars of peas (broadly distributed) and two lines were used in a strip-plot design. Significant positive correlations were detected between forage yield and some other traits. This way, forage yield stability may be indirectly improved by improving certain traits showing qualitative inheritance. Comparisons revealed that genotypes exhibited stable performance, even in low-input farming systems. AMMI analysis, GGE biplot, and analysis of variance (ANOVA) combination showed statistically significant differences between genotypes and environments and the farming system. Our analysis depicted specific cultivars of peas for different areas and farming systems to attain highly stable performance. Vermio was confirmed to be a stable genotype for forage yield performance in low-input farming in Trikala and Kalambaka areas, while Pisso was indicated as the best in Florina and Giannitsa areas in low-input farming. The two pea lines exhibited stable performance in Giannitsa and Florina areas, especially in low-input conditions. The stable behavior of some genotypes in these conditions may be useful for farmers that raise livestock in mountainous areas. The genetic parameters show that the selection for fresh forage yield and dry matter yield in breeding programs is expected to be effective. Full article
(This article belongs to the Special Issue Legume Genomics and Breeding)
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16 pages, 2536 KiB  
Article
The First Genetic Linkage Map of Winged Bean [Psophocarpus tetragonolobus (L.) DC.] and QTL Mapping for Flower-, Pod-, and Seed-Related Traits
Plants 2022, 11(4), 500; https://doi.org/10.3390/plants11040500 - 12 Feb 2022
Cited by 6 | Viewed by 2169
Abstract
Winged bean [Psophocarpus tetragonolobus (L.) DC.] (2n = 2× = 18) is a tropical legume crop with multipurpose usages. Recently, the winged bean has regained attention from scientists as a food protein source. Currently, there is no breeding program for winged bean [...] Read more.
Winged bean [Psophocarpus tetragonolobus (L.) DC.] (2n = 2× = 18) is a tropical legume crop with multipurpose usages. Recently, the winged bean has regained attention from scientists as a food protein source. Currently, there is no breeding program for winged bean cultivars. All winged bean cultivars are landraces or selections from landraces. Molecular markers and genetic linkage maps are pre-requisites for molecular plant breeding. The aim of this study was to develop a high-density linkage map and identify quantitative trait loci (QTLs) for pod and seed-related traits of the winged bean. An F2 population of 86 plants was developed from a cross between winged bean accessions W054 and TPT9 showing contrasting pod length, and pod, flower and seed colors. A genetic linkage map of 1384 single nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing was constructed. The map resolved nine haploid chromosomes of the winged bean and spanned the cumulative length of 4552.8 cM with the number of SNPs per linkage ranging from 36 to 218 with an average of 153.78. QTL analysis in the F2 population revealed 31 QTLs controlling pod length, pod color, pod anthocyanin content, flower color, and seed color. The number of QTLs per trait varied between 1 (seed length) to 7 (banner color). Interestingly, the major QTLs for pod color, anthocyanin content, and calyx color, and for seed color and flower wing color were located at the same position. The high-density linkage map QTLs reported in this study will be useful for molecular breeding of winged beans. Full article
(This article belongs to the Special Issue Legume Genomics and Breeding)
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22 pages, 1190 KiB  
Article
Adaptability and Stability of Faba Bean (Vicia faba L.) Accessions under Diverse Environments and Herbicide Treatments
Plants 2022, 11(3), 251; https://doi.org/10.3390/plants11030251 - 19 Jan 2022
Cited by 10 | Viewed by 2201
Abstract
The adaptability and stability of 37 faba bean (Vicia faba L.) accessions with different levels of tolerance to metribuzin or imazethapyr was assessed across 12 season–location–herbicide experiments. Significant Genotype x environment (GE) interaction was found for the days to flowering (DFLR), plant [...] Read more.
The adaptability and stability of 37 faba bean (Vicia faba L.) accessions with different levels of tolerance to metribuzin or imazethapyr was assessed across 12 season–location–herbicide experiments. Significant Genotype x environment (GE) interaction was found for the days to flowering (DFLR), plant height (PLHT) and grain yield (GY). Performance and stability of the accessions regarding PLHT and GY were assessed using four different stability parameters: cultivar superiority, static stability, Wricke’s eco-valence and Finlay and Wilkinson’s regression model. The stability parameters ranked these genotypes differently suggesting that PLHT and GY stability should be assessed not only on a single or a few stability parameters but on a combination of them. GGE biplot analysis indicated that the environments representing metribuzin treatment at Marchouch 2014–2015 and the non-treated treatment at Terbol 2018–2019 are the ideal environments for evaluating faba bean genotypes. GGE biplots showed herbicide tolerant accession IG12983 with simultaneous average PLHT, GY and stability across the environments. The performance of other tolerant accessions, namely IG13945, IG13906, IG106453, FB2648, and FB1216 was less stable but superior under specific mega environments. Therefore, utilizing these accessions in faba bean breeding programs would help broaden the adaptability to diverse locations–season–herbicide treatments. Full article
(This article belongs to the Special Issue Legume Genomics and Breeding)
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21 pages, 1844 KiB  
Article
Sources of Resistance to Common Bacterial Blight and Charcoal Rot Disease for the Production of Mesoamerican Common Beans in the Southern United States
Plants 2021, 10(5), 998; https://doi.org/10.3390/plants10050998 - 17 May 2021
Cited by 7 | Viewed by 2632
Abstract
The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern [...] Read more.
The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) to evaluate field-level resistance from the various commercial classes and subgroups represented in the Mesoamerican gene pool as sources for breeding beans for the region and (2) to evaluate genome-wide marker × trait associations (GWAS) using genetic markers for the genotypes. A total of 300 genotypes from the Mesoamerican Diversity Panel (MDP) were evaluated for CBB and CR in field experiments for three years. CBB resistance was also tested with a field isolate in controlled greenhouse conditions. The analysis of variance revealed the presence of variability in the MDP for the evaluated traits. We also identified adapted common bean genotypes that could be used directly in Southeastern production or that could be good parents in breeding programs for CBB and CR resistance. The GWAS detected 14 significant Single-Nucleotide Polymorphism (SNP) markers associated with CBB resistance distributed on five chromosomes, namely Pv02, Pv04, Pv08, Pv10, and Pv11, but no loci for resistance to CR. A total of 89 candidate genes were identified in close vicinity (±100 kb) to the significant CBB markers, some of which could be directly or indirectly involved in plant defense to diseases. These results provide a basis to further understand the complex inheritance of CBB resistance in Mesoamerican common beans and show that this biotic stress is unrelated to CR resistance, which was evident during a drought period. Genotypes with good yield potential for the Southeastern U.S. growing conditions were found with resistant to infection by the two diseases, as well as adaptation to the hot and humid conditions punctuated by droughts found in this region. Full article
(This article belongs to the Special Issue Legume Genomics and Breeding)
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