1
|
Mwale SE, Shimelis H, Abincha W, Nkhata W, Sefasi A, Mashilo J. Genetic differentiation of a southern Africa tepary bean (Phaseolus acutifolius A Gray) germplasm collection using high-density DArTseq SNP markers. PLoS One 2023; 18:e0295773. [PMID: 38096255 PMCID: PMC10721083 DOI: 10.1371/journal.pone.0295773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Genetic resources of tepary bean (Phaseolus acutifolius A. Gray) germplasm collections are not well characterized due to a lack of dedicated genomic resources. There is a need to assemble genomic resources specific to tepary bean for germplasm characterization, heterotic grouping, and breeding. Therefore, the objectives of this study were to deduce the genetic groups in tepary bean germplasm collection using high-density Diversity Array Technology (DArT) based single nucleotide polymorphism (SNP) markers and select contrasting genotypes for breeding. Seventy-eight tepary bean accessions were genotyped using 10527 SNPs markers, and genetic parameters were estimated. Population structure was delineated using principal component and admixture analyses. A mean polymorphic information content (PIC) of 0.27 was recorded, indicating a relatively low genetic resolution of the developed SNPs markers. Low genetic variation (with a genetic distance [GD] = 0.32) existed in the assessed tepary bean germplasm collection. Population structure analysis identified five sub-populations through sparse non-negative matrix factorization (snmf) with high admixtures. Analysis of molecular variance indicated high genetic differentiation within populations (61.88%) and low between populations (38.12%), indicating high gene exchange. The five sub-populations exhibited variable fixation index (FST). The following genetically distant accessions were selected: Cluster 1:Tars-Tep 112, Tars-Tep 10, Tars-Tep 23, Tars-Tep-86, Tars-Tep-83, and Tars-Tep 85; Cluster 3: G40022, Tars-Tep-93, and Tars-Tep-100; Cluster 5: Zimbabwe landrace, G40017, G40143, and G40150. The distantly related and contrasting accessions are useful to initiate crosses to enhance genetic variation and for the selection of economic traits in tepary bean.
Collapse
Affiliation(s)
- Saul Eric Mwale
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Biological Sciences Department, The African Centre of Excellence in Neglected and Underutilized Biodiversity (ACENUB), Mzuzu University, Luwinga, Mzuzu, Malawi
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Wilfred Abincha
- Kenya Agricultural and Livestock Research Organization (KALRO), Non-Ruminant Research Institute, Kakamega, Kenya
| | - Wilson Nkhata
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Alliance of Bioversity International Institute of Tropical Agriculture (CIAT), Chitedze Agricultural Station, Lilongwe, Malawi
| | - Abel Sefasi
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Jacob Mashilo
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
| |
Collapse
|
2
|
Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
Collapse
Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
3
|
Barrera S, Berny Mier y Teran JC, Lobaton JD, Escobar R, Gepts P, Beebe S, Urrea CA. Large genomic introgression blocks of Phaseolus parvifolius Freytag bean into the common bean enhance the crossability between tepary and common beans. PLANT DIRECT 2022; 6:e470. [PMID: 36523608 PMCID: PMC9745863 DOI: 10.1002/pld3.470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 06/10/2023]
Abstract
The production of the common bean (Phaseolus vulgaris L.), one of the most important sources of protein and minerals and one of the most consumed grain legumes globally, is highly affected by heat and drought constraints. In contrast, the tepary bean (Phaseolus acutifolius A. Gray), a common bean-related species, is adapted to hot and dry climates. Hybridization to introduce complex traits from the tepary bean into the common bean has been challenging, as embryo rescue is required. In this study, we report three novel interspecific lines that were obtained by crossing lines from prior common bean × tepary bean hybridization with Phaseolus parvifolius Freytag in order to increase the male gametic diversity to facilitate interspecific crosses. These interspecific lines enhanced the crossability of the common bean and tepary bean species while avoiding the embryo rescue process. Crossing these three interspecific lines with tepary beans resulted in 12-fold more hybrid plants than crossing traditional common beans with tepary beans. Whole-genome sequencing analysis of these three interspecific lines shows large introgressions of genomic regions corresponding to P. parvifolius on chromosomes that presumably contribute to reproductive barriers between both species. The development of these lines opens up the possibility of increasing the introgression of desirable tepary bean traits into the common bean to address constraints driven by climate change.
Collapse
Affiliation(s)
- Santos Barrera
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNebraskaUSA
| | | | - Juan David Lobaton
- Department of Evolutionary BiologyNational Australian UniversityCanberraAustralia
| | | | - Paul Gepts
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Steve Beebe
- International Center for Tropical Agriculture (CIAT)PalmiraColombia
| | - Carlos A. Urrea
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNebraskaUSA
| |
Collapse
|
4
|
Taboada G, Abán CL, Mercado Cárdenas G, Spedaletti Y, Aparicio González M, Maita E, Ortega-Baes P, Galván M. Characterization of fungal pathogens and germplasm screening for disease resistance in the main production area of the common bean in Argentina. FRONTIERS IN PLANT SCIENCE 2022; 13:986247. [PMID: 36161011 PMCID: PMC9490223 DOI: 10.3389/fpls.2022.986247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet, mainly in Africa and Latin America. Argentina is one of the five major producers of the common bean in the world, and the main cultivation areas are concentrated in the northwestern provinces of this country. Crop production of the common bean is often affected by biotic factors like some endemic fungal diseases, which exert a major economic impact on the region. The most important fungal diseases affecting the common bean in Argentina are white mold caused by Sclerotinia sclerotiorum, angular leaf spot caused by Pseudocercospora griseola, web blight and root rot caused by Rhizoctonia solani, which can cause production losses of up to 100% in the region. At the present, the most effective strategy for controlling these diseases is the use of genetic resistance. In this sense, population study and characterization of fungal pathogens are essential for developing cultivars with durable resistance. In this review we report diversity studies carried out on these three fungal pathogens affecting the common bean in northwestern Argentina, analyzing more than 200 isolates by means of molecular, morphological and pathogenic approaches. Also, the screening of physiological resistance in several common bean commercial lines and wild native germplasm is reviewed. This review contributes to the development of sustainable management strategies and cultural practices in bean production aimed to minimize yield losses due to fungal diseases in the common bean.
Collapse
Affiliation(s)
- Gisel Taboada
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Carla L. Abán
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | | | - Yamila Spedaletti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Mónica Aparicio González
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Efrain Maita
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Pablo Ortega-Baes
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Marta Galván
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| |
Collapse
|
5
|
Chongtham SK, Devi EL, Samantara K, Yasin JK, Wani SH, Mukherjee S, Razzaq A, Bhupenchandra I, Jat AL, Singh LK, Kumar A. Orphan legumes: harnessing their potential for food, nutritional and health security through genetic approaches. PLANTA 2022; 256:24. [PMID: 35767119 DOI: 10.1007/s00425-022-03923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Legumes, being angiosperm's third-largest family as well as the second major crop family, contributes beyond 33% of human dietary proteins. The advent of the global food crisis owing to major climatic concerns leads to nutritional deprivation, hunger and hidden hunger especially in developing and underdeveloped nations. Hence, in the wake of promoting sustainable agriculture and nutritional security, apart from the popular legumes, the inclusion of lesser-known and understudied local crop legumes called orphan legumes in the farming systems of various tropical and sub-tropical parts of the world is indeed a need of the hour. Despite possessing tremendous potentialities, wide adaptability under diverse environmental conditions, and rich in nutritional and nutraceutical values, these species are still in a neglected and devalued state. Therefore, a major re-focusing of legume genetics, genomics, and biology is much crucial in pursuance of understanding the yield constraints, and endorsing underutilized legume breeding programs. Varying degrees of importance to these crops do exist among researchers of developing countries in establishing the role of orphan legumes as future crops. Under such circumstances, this article assembles a comprehensive note on the necessity of promoting these crops for further investigations and sustainable legume production, the exploitation of various orphan legume species and their potencies. In addition, an attempt has been made to highlight various novel genetic, molecular, and omics approaches for the improvement of such legumes for enhancing yield, minimizing the level of several anti-nutritional factors, and imparting biotic and abiotic stress tolerance. A significant genetic enhancement through extensive research in 'omics' areas is the absolute necessity to transform them into befitting candidates for large-scale popularization around the globe.
Collapse
Affiliation(s)
- Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, CAEPHT, CAU, Ranipool, Gangtok, Sikkim, 737135, India
| | | | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Odisha, 761211, India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, 192101, Jammu and Kashmir, India.
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West Bengal, 742213, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Ingudam Bhupenchandra
- ICAR-KVK Tamenglong, ICAR RC for NEH Region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Aanandi Lal Jat
- Castor-Mustard Research Station, SDAU, S.K. Nagar, Banaskantha, Gujarat, 385 506, India
| | - Laishram Kanta Singh
- ICAR-KVK Imphal West, ICAR RC for NEH region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Amit Kumar
- ICAR Research Complex for NEH Region, Tadong, Sikkim Centre, 737102, India
| |
Collapse
|
6
|
Moghaddam SM, Oladzad A, Koh C, Ramsay L, Hart JP, Mamidi S, Hoopes G, Sreedasyam A, Wiersma A, Zhao D, Grimwood J, Hamilton JP, Jenkins J, Vaillancourt B, Wood JC, Schmutz J, Kagale S, Porch T, Bett KE, Buell CR, McClean PE. The tepary bean genome provides insight into evolution and domestication under heat stress. Nat Commun 2021; 12:2638. [PMID: 33976152 PMCID: PMC8113540 DOI: 10.1038/s41467-021-22858-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/07/2021] [Indexed: 02/03/2023] Open
Abstract
Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.
Collapse
Affiliation(s)
- Samira Mafi Moghaddam
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Plant Resilience Institute, Michigan State University, East Lansing, MI USA
| | - Atena Oladzad
- grid.261055.50000 0001 2293 4611Department of Plant Sciences and Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND USA
| | - Chushin Koh
- grid.25152.310000 0001 2154 235XDepartment of Plant Sciences, University of Saskatchewan, Saskatoon, SK Canada ,grid.25152.310000 0001 2154 235XGlobal Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK Canada
| | - Larissa Ramsay
- grid.25152.310000 0001 2154 235XDepartment of Plant Sciences, University of Saskatchewan, Saskatoon, SK Canada
| | - John P. Hart
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, PR USA
| | - Sujan Mamidi
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Genevieve Hoopes
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA
| | - Avinash Sreedasyam
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Andrew Wiersma
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Plant Resilience Institute, Michigan State University, East Lansing, MI USA
| | - Dongyan Zhao
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA
| | - Jane Grimwood
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA ,grid.184769.50000 0001 2231 4551US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - John P. Hamilton
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA
| | - Jerry Jenkins
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA ,grid.184769.50000 0001 2231 4551US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Brieanne Vaillancourt
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA
| | - Joshua C. Wood
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA
| | - Jeremy Schmutz
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA ,grid.184769.50000 0001 2231 4551US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Sateesh Kagale
- grid.24433.320000 0004 0449 7958National Research Council Canada, Saskatoon, SK Canada
| | - Timothy Porch
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, PR USA
| | - Kirstin E. Bett
- grid.25152.310000 0001 2154 235XDepartment of Plant Sciences, University of Saskatchewan, Saskatoon, SK Canada
| | - C. Robin Buell
- grid.17088.360000 0001 2150 1785Department of Plant Biology, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Plant Resilience Institute, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Michigan State University AgBioResearch, East Lansing, MI USA
| | - Phillip E. McClean
- grid.261055.50000 0001 2293 4611Department of Plant Sciences and Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND USA
| |
Collapse
|
7
|
Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives. Genes (Basel) 2021; 12:genes12040556. [PMID: 33921270 PMCID: PMC8070098 DOI: 10.3390/genes12040556] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/01/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between Mexico and the United States. Therefore, we hypothesize that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, we determined the genotype x environmental association (GEA) of each gene. Diversity analysis found that cultivated and wild P. acutifolius were intermingled with var. tenuifolius and P. parvifolius, signifying that allele diversity was ample in the wild and cultivated clade over a broad sense (sensu lato) evaluation. Genes Dreb2B and ERECTA harbored signatures of directional selection, represented by six SNPs correlated with the environmental drought indices. This suggests that wild tepary bean is a reservoir of novel alleles at genes for drought tolerance, as expected for a species that originated in arid environments. Our study corroborated that candidate gene approach was effective for marker validation across a broad genetic base of wild tepary accessions.
Collapse
|
8
|
Delfini J, Moda-Cirino V, dos Santos Neto J, Ruas PM, Sant’Ana GC, Gepts P, Gonçalves LSA. Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Sci Rep 2021; 11:2964. [PMID: 33536468 PMCID: PMC7859210 DOI: 10.1038/s41598-021-82437-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.
Collapse
Affiliation(s)
- Jessica Delfini
- grid.411400.00000 0001 2193 3537Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil ,Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - Vânia Moda-Cirino
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - José dos Santos Neto
- grid.411400.00000 0001 2193 3537Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil ,Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - Paulo Maurício Ruas
- grid.411400.00000 0001 2193 3537Biology Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil
| | | | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, 95616-8780 USA
| | | |
Collapse
|
9
|
Pratap A, Das A, Kumar S, Gupta S. Current Perspectives on Introgression Breeding in Food Legumes. FRONTIERS IN PLANT SCIENCE 2020; 11:589189. [PMID: 33552095 PMCID: PMC7858677 DOI: 10.3389/fpls.2020.589189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/03/2020] [Indexed: 05/22/2023]
Abstract
Food legumes are important for defeating malnutrition and sustaining agri-food systems globally. Breeding efforts in legume crops have been largely confined to the exploitation of genetic variation available within the primary genepool, resulting in narrow genetic base. Introgression as a breeding scheme has been remarkably successful for an array of inheritance and molecular studies in food legumes. Crop wild relatives (CWRs), landraces, and exotic germplasm offer great potential for introgression of novel variation not only to widen the genetic base of the elite genepool for continuous incremental gains over breeding cycles but also to discover the cryptic genetic variation hitherto unexpressed. CWRs also harbor positive quantitative trait loci (QTLs) for improving agronomic traits. However, for transferring polygenic traits, "specialized population concept" has been advocated for transferring QTLs from CWR into elite backgrounds. Recently, introgression breeding has been successful in developing improved cultivars in chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), peanut (Arachis hypogaea), lentil (Lens culinaris), mungbean (Vigna radiata), urdbean (Vigna mungo), and common bean (Phaseolus vulgaris). Successful examples indicated that the usable genetic variation could be exploited by unleashing new gene recombination and hidden variability even in late filial generations. In mungbean alone, distant hybridization has been deployed to develop seven improved commercial cultivars, whereas in urdbean, three such cultivars have been reported. Similarly, in chickpea, three superior cultivars have been developed from crosses between C. arietinum and Cicer reticulatum. Pigeonpea has benefited the most where different cytoplasmic male sterility genes have been transferred from CWRs, whereas a number of disease-resistant germplasm have also been developed in Phaseolus. As vertical gene transfer has resulted in most of the useful gene introgressions of practical importance in food legumes, the horizontal gene transfer through transgenic technology, somatic hybridization, and, more recently, intragenesis also offer promise. The gains through introgression breeding are significant and underline the need of bringing it in the purview of mainstream breeding while deploying tools and techniques to increase the recombination rate in wide crosses and reduce the linkage drag. The resurgence of interest in introgression breeding needs to be capitalized for development of commercial food legume cultivars.
Collapse
Affiliation(s)
- Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Arpita Das
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
- *Correspondence: Sanjeev Gupta,
| | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kanpur, India
- Shiv Kumar,
| |
Collapse
|
10
|
Zargar SM, Mahajan R, Nazir M, Nagar P, Kim ST, Rai V, Masi A, Ahmad SM, Shah RA, Ganai NA, Agrawal GK, Rakwal R. Common bean proteomics: Present status and future strategies. J Proteomics 2017; 169:239-248. [DOI: 10.1016/j.jprot.2017.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 11/30/2022]
|
11
|
Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
Collapse
Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
| |
Collapse
|
12
|
Bitocchi E, Rau D, Bellucci E, Rodriguez M, Murgia ML, Gioia T, Santo D, Nanni L, Attene G, Papa R. Beans ( Phaseolus ssp.) as a Model for Understanding Crop Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:722. [PMID: 28533789 PMCID: PMC5420584 DOI: 10.3389/fpls.2017.00722] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.
Collapse
Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Domenico Rau
- Department of Agriculture, University of SassariSassari, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | | | - Maria L. Murgia
- Department of Agriculture, University of SassariSassari, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of BasilicataPotenza, Italy
| | - Debora Santo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Giovanna Attene
- Department of Agriculture, University of SassariSassari, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| |
Collapse
|
13
|
Bhawna, Bonthala VS, Gajula MP. PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw114. [PMID: 27465131 PMCID: PMC4962766 DOI: 10.1093/database/baw114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/07/2016] [Indexed: 11/18/2022]
Abstract
The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely. Database URL:http://www.multiomics.in/PvTFDB/
Collapse
Affiliation(s)
- Bhawna
- Institute of Biotechnology, PJTSAU, Rajendra Nagar, Hyderabad 500030, India
| | - V S Bonthala
- Institute of Biotechnology, PJTSAU, Rajendra Nagar, Hyderabad 500030, India
| | - Mnv Prasad Gajula
- Institute of Biotechnology, PJTSAU, Rajendra Nagar, Hyderabad 500030, India
| |
Collapse
|