1
|
Raggi L, Caproni L, Ciancaleoni S, D'Amato R, Businelli D, Negri V. Investigating the genetic basis of salt-tolerance in common bean: a genome-wide association study at the early vegetative stage. Sci Rep 2024; 14:5315. [PMID: 38438439 PMCID: PMC10912697 DOI: 10.1038/s41598-024-55403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Salinity poses a significant challenge to global crop productivity, affecting approximately 20% of cultivated and 33% of irrigated farmland, and this issue is on the rise. Negative impact of salinity on plant development and metabolism leads to physiological and morphological alterations mainly due to high ion concentration in tissues and the reduced water and nutrients uptake. Common bean (Phaseolus vulgaris L.), a staple food crop accounting for a substantial portion of consumed grain legumes worldwide, is highly susceptible to salt stress resulting in noticeable reduction in dry matter gain in roots and shoots even at low salt concentrations. In this study we screened a common bean panel of diversity encompassing 192 homozygous genotypes for salt tolerance at seedling stage. Phenotypic data were leveraged to identify genomic regions involved in salt stress tolerance in the species through GWAS. We detected seven significant associations between shoot dry weight and SNP markers. The candidate genes, in linkage with the regions associated to salt tolerance or harbouring the detected SNP, showed strong homology with genes known to be involved in salt tolerance in Arabidopsis. Our findings provide valuable insights onto the genetic control of salt tolerance in common bean and represent a first contribution to address the challenge of salinity-induced yield losses in this species and poses the ground to eventually breed salt tolerant common bean varieties.
Collapse
Affiliation(s)
- Lorenzo Raggi
- Dipartimento di Scienze Agrarie Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy.
| | - Leonardo Caproni
- Dipartimento di Scienze Agrarie Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Simona Ciancaleoni
- Dipartimento di Scienze Agrarie Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Roberto D'Amato
- Dipartimento di Scienze Agrarie Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Daniela Businelli
- Dipartimento di Scienze Agrarie Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Valeria Negri
- Dipartimento di Scienze Agrarie Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| |
Collapse
|
2
|
Hamabwe SM, Otieno NA, Soler-Garzón A, Miklas PN, Parker T, Kramer DM, Chattopadhyay A, Cheelo P, Kuwabo K, Kamfwa K. Identification of quantitative trait loci for drought tolerance in Bukoba/Kijivu Andean mapping population of common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:222. [PMID: 37823979 DOI: 10.1007/s00122-023-04463-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE Quantitative Trait Loci "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07 and Pv10 of common bean. Drought is a major production constraint of common bean (Phaseolus vulgaris L.) worldwide. The objective of this study was to identify the Quantitative Trait Loci (QTL) for drought tolerance in an Andean population of Recombinant Inbred Lines (RILs). A total of 155 F5:7 RILs derived from a cross between Kijivu (drought tolerant) and Bukoba (drought susceptible) were evaluated for drought tolerance in field and pot experiments. Four field experiments were conducted at three locations in Zambia in 2020 and 2021. All field trials were conducted in the dry season under irrigation. The 155 RILs were genotyped with 11,292 SNPs, and composite interval mapping was conducted to identify QTL for drought tolerance. Seed yield for Kijivu under drought stress was consistently higher than for Bukoba across all four field trials. A total of 60 QTL were identified for morphological, agronomic, and physiological traits under drought stress and non-stress conditions. However, the majority of these QTL were specific to drought stress. QTL "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07, and Pv10. Extensive co-localizations for agronomic and morpho-physiological traits under drought stress were observed at the three drought-tolerance QTL hotspots. Additionally, these three QTL hotspots overlapped with previously identified QTL for drought tolerance, while several others identified QTL are novel. The three identified QTL hotspots could be used in future marker-assisted selection for drought tolerance in common bean.
Collapse
Affiliation(s)
- Swivia M Hamabwe
- Department of Biology, School of Science and Technology, University of Nairobi, Nairobi, Kenya
- Department of Plant Science, University of Zambia, Great East Road, Lusaka, Zambia
| | - Nicholas Amimo Otieno
- Department of Biology, School of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Alvaro Soler-Garzón
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture-Agricultural Research Service, Prosser, WA, USA
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture-Agricultural Research Service, Prosser, WA, USA
| | - Travis Parker
- Department of Plant Sciences/MS1, Section of Crop and Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - David M Kramer
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Pride Cheelo
- Department of Plant Science, University of Zambia, Great East Road, Lusaka, Zambia
| | - Kuwabo Kuwabo
- Department of Plant Science, University of Zambia, Great East Road, Lusaka, Zambia
| | - Kelvin Kamfwa
- Department of Plant Science, University of Zambia, Great East Road, Lusaka, Zambia.
| |
Collapse
|
3
|
Labastida D, Ingvarsson PK, Rendón-Anaya M. Dissecting the genetic basis of drought responses in common bean using natural variation. FRONTIERS IN PLANT SCIENCE 2023; 14:1143873. [PMID: 37780498 PMCID: PMC10538545 DOI: 10.3389/fpls.2023.1143873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/27/2023] [Indexed: 10/03/2023]
Abstract
The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional "stay-green" (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes.
Collapse
Affiliation(s)
- Diana Labastida
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Pär K. Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Martha Rendón-Anaya
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| |
Collapse
|
4
|
de Souza IP, de Azevedo BR, Coelho ASG, de Souza TLPO, Valdisser PAMR, Gomes-Messias LM, Funicheli BO, Brondani C, Vianello RP. Whole-genome resequencing of common bean elite breeding lines. Sci Rep 2023; 13:12721. [PMID: 37543642 PMCID: PMC10404220 DOI: 10.1038/s41598-023-39399-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing-WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs.
Collapse
Affiliation(s)
- Isabela Pavanelli de Souza
- Genetics and Plant Breeding, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil.
| | - Beatriz Rosa de Azevedo
- Biotechnology, Scientific Initiation Scholarship, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil
| | | | | | | | | | | | - Claudio Brondani
- Molecular Biology, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil
| | - Rosana Pereira Vianello
- Molecular Biology, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil
| |
Collapse
|
5
|
Cruz S, Lobatón J, Urban MO, Ariza-Suarez D, Raatz B, Aparicio J, Mosquera G, Beebe S. Interspecific common bean population derived from Phaseolus acutifolius using a bridging genotype demonstrate useful adaptation to heat tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1145858. [PMID: 37293677 PMCID: PMC10246688 DOI: 10.3389/fpls.2023.1145858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/18/2023] [Indexed: 06/10/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide and is a major nutrient source in the tropics. Common bean reproductive development is strongly affected by heat stress, particularly overnight temperatures above 20°C. The desert Tepary bean (Phaseolus acutifolius A. Gray) offers a promising source of adaptative genes due to its natural acclimation to arid conditions. Hybridization between both species is challenging, requiring in vitro embryo rescue and multiple backcrossing cycles to restore fertility. This labor-intensive process constrains developing mapping populations necessary for studying heat tolerance. Here we show the development of an interspecific mapping population using a novel technique based on a bridging genotype derived from P. vulgaris, P. Acutifolius and P. parvifolius named VAP1 and is compatible with both common and tepary bean. The population was based on two wild P. acutifolius accessions, repeatedly crossed with Mesoamerican elite common bush bean breeding lines. The population was genotyped through genotyping-by-sequencing and evaluated for heat tolerance by genome-wide association studies. We found that the population harbored 59.8% introgressions from wild tepary, but also genetic regions from Phaseolus parvifolius, a relative represented in some early bridging crosses. We found 27 significative quantitative trait loci, nine located inside tepary introgressed segments exhibiting allelic effects that reduced seed weight, and increased the number of empty pods, seeds per pod, stem production and yield under high temperature conditions. Our results demonstrate that the bridging genotype VAP1 can intercross common bean with tepary bean and positively influence the physiology of derived interspecific lines, which displayed useful variance for heat tolerance.
Collapse
|
6
|
Gutiérrez N, Pégard M, Balko C, Torres AM. Genome-wide association analysis for drought tolerance and associated traits in faba bean ( Vicia faba L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1091875. [PMID: 36818887 PMCID: PMC9928957 DOI: 10.3389/fpls.2023.1091875] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Faba bean (Vicia faba L.) is an important high protein legume adapted to diverse climatic conditions with multiple benefits for the overall sustainability of the cropping systems. Plant-based protein demand is being expanded and faba bean is a good candidate to cover this need. However, the crop is very sensitive to abiotic stresses, especially drought, which severely affects faba bean yield and development worldwide. Therefore, identifying genes associated with drought stress tolerance is a major challenge in faba bean breeding. Although the faba bean response to drought stress has been widely studied, the molecular approaches to improve drought tolerance in this crop are still limited. Here we built on recent genomic advances such as the development of the first high-density SNP genotyping array, to conduct a genome-wide association study (GWAS) using thousands of genetic polymorphisms throughout the entire faba bean genome. A worldwide collection of 100 faba bean accessions was grown under control and drought conditions and 10 morphological, phenological and physiological traits were evaluated to identify single nucleotide polymorphism (SNP) markers associated with drought tolerance. We identified 29 SNP markers significantly correlated with these traits under drought stress conditions. The flanking sequences were blasted to the Medicago truncatula reference genomes in order to annotate potential candidate genes underlying the causal variants. Three of the SNPs for chlorophyll content after the stress, correspond to uncharacterized proteins indicating the presence of novel genes associated with drought tolerance in faba bean. The significance of stress-inducible signal transducers provides valuable information on the possible mechanisms underlying the faba bean response to drought stress, thus providing a foundation for future marker-assisted breeding in the crop.
Collapse
Affiliation(s)
- Natalia Gutiérrez
- Área de Mejora y Biotecnología, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Centro Alameda del Obispo, Córdoba, Spain
| | - Marie Pégard
- INRAE P3F, 86600 Lusignan, France, INRA, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | - Christiane Balko
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Ana M. Torres
- Área de Mejora y Biotecnología, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Centro Alameda del Obispo, Córdoba, Spain
| |
Collapse
|
7
|
Arriagada O, Arévalo B, Cabeza RA, Carrasco B, Schwember AR. Meta-QTL Analysis for Yield Components in Common Bean ( Phaseolus vulgaris L.). PLANTS (BASEL, SWITZERLAND) 2022; 12:117. [PMID: 36616246 PMCID: PMC9824219 DOI: 10.3390/plants12010117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
Collapse
Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| |
Collapse
|
8
|
Gomes-Messias LM, Vianello RP, Marinho GR, Rodrigues LA, Coelho AG, Pereira HS, Melo LC, de Souza TLPO. Genetic mapping of the Andean anthracnose resistance gene present in the common bean cultivar BRSMG Realce. FRONTIERS IN PLANT SCIENCE 2022; 13:1033687. [PMID: 36507385 PMCID: PMC9728541 DOI: 10.3389/fpls.2022.1033687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
The rajado seeded Andean bean (Phaseolus vulgaris L.) cultivar BRSMG Realce (striped seed coat) developed by Embrapa expressed a high level of anthracnose resistance, caused by Colletotrichum lindemuthianum, in field and greenhouse screenings. The main goal of this study was to evaluate the inheritance of anthracnose resistance in BRSMG Realce, map the resistance locus or major gene cluster previously named as Co-Realce, identify resistance-related positional genes, and analyze potential markers linked to the resistance allele. F2 plants derived from the cross BRSMG Realce × BRS FC104 (Mesoamerican) and from the cross BRSMG Realce × BRS Notável (Mesoamerican) were inoculated with the C. lindemuthianum races 475 and 81, respectively. The BRSMG Realce × BRS FC104 F2 population was also genotyped using the DArTseq technology. Crosses between BRSMG Realce and BAT 93 (Mesoamerican) were also conducted and resulting F2 plants were inoculated with the C. lindemuthianum races 65 and 1609, individually. The results shown that anthracnose resistance in BRSMG Realce is controlled by a single locus with complete dominance. A genetic map including 1,118 SNP markers was built and shown 78% of the markers mapped at a distances less than 5.0 cM, with a total genetic length of 4,473.4 cM. A major locus (Co-Realce) explaining 54.6% of the phenotypic variation of symptoms caused by the race 475 was identified in Pv04, flanked by the markers snp1327 and snp12782 and 4.48 cM apart each other. These SNPs are useful for marker-assisted selection, due to an estimated selection efficiency of 99.2%. The identified resistance allele segregates independently of the resistance allele Co-33 (Pv04) present in BAT 93. The mapped genomic region with 704,867 bp comprising 63 putative genes, 44 of which were related to the pathogen-host interaction. Based on all these results and evidence, anthracnose resistance in BRSMG Realce should be considered as monogenic, useful for breeding purpose. It is proposed that locus Co-Realce is unique and be provisionally designated as CoPv04R until be officially nominated in accordance with the rules established by the Bean Improvement Cooperative Genetics Committee.
Collapse
|
9
|
Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
Collapse
Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
| |
Collapse
|
10
|
Zia B, Shi A, Olaoye D, Xiong H, Ravelombola W, Gepts P, Schwartz HF, Brick MA, Otto K, Ogg B, Chen S. Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean ( Phaseolus vulgaris) Core Collection. Front Genet 2022; 13:853114. [PMID: 35711938 PMCID: PMC9197503 DOI: 10.3389/fgene.2022.853114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.
Collapse
Affiliation(s)
- Bazgha Zia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Dotun Olaoye
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Waltram Ravelombola
- Organic & Specialty Crop Breeding, Texas A&M AgriLife Research, Vernon, TX, United States
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, Davis, CA, United States
| | - Howard F Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kristen Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Barry Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Senyu Chen
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, United States
| |
Collapse
|
11
|
Lv Y, Ma J, Wei H, Xiao F, Wang Y, Jahan N, Hazman M, Qian Q, Shang L, Guo L. Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:912637. [PMID: 35783926 PMCID: PMC9248812 DOI: 10.3389/fpls.2022.912637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 05/12/2023]
Abstract
Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.
Collapse
Affiliation(s)
- Yang Lv
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Ma
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Wei
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fang Xiao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yueying Wang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Noushin Jahan
- Department of Agronomy, Khulna Agricultural University, Khulna, Bangladesh
| | - Mohamed Hazman
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Longbiao Guo,
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Longbiao Guo,
| |
Collapse
|
12
|
Losa A, Vorster J, Cominelli E, Sparvoli F, Paolo D, Sala T, Ferrari M, Carbonaro M, Marconi S, Camilli E, Reboul E, Waswa B, Ekesa B, Aragão F, Kunert K. Drought and heat affect common bean minerals and human diet—What we know and where to go. Food Energy Secur 2021. [DOI: 10.1002/fes3.351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Alessia Losa
- Council for Research in Agriculture and Economics Research Centre for Genomics and Bioinformatics (CREA‐GB) Montanaso Italy
| | - Juan Vorster
- Department Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
| | - Eleonora Cominelli
- National Research Council Institute of Agricultural Biology and Biotechnology (CNR‐IBBA) Milan Italy
| | - Francesca Sparvoli
- National Research Council Institute of Agricultural Biology and Biotechnology (CNR‐IBBA) Milan Italy
| | - Dario Paolo
- National Research Council Institute of Agricultural Biology and Biotechnology (CNR‐IBBA) Milan Italy
| | - Tea Sala
- Council for Research in Agriculture and Economics Research Centre for Genomics and Bioinformatics (CREA‐GB) Montanaso Italy
| | - Marika Ferrari
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | - Marina Carbonaro
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | - Stefania Marconi
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | - Emanuela Camilli
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | | | - Boaz Waswa
- International Center for Tropical Agriculture (CIAT) CIAT Regional Office for Africa Nairobi Kenya
| | - Beatrice Ekesa
- International Center for Tropical Agriculture (CIAT) CIAT Regional Office for Africa Nairobi Kenya
| | | | - Karl Kunert
- Department Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
| |
Collapse
|
13
|
Delfini J, Moda-Cirino V, dos Santos Neto J, Zeffa DM, Nogueira AF, Ribeiro LAB, Ruas PM, Gepts P, Gonçalves LSA. Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:748829. [PMID: 34691125 PMCID: PMC8528967 DOI: 10.3389/fpls.2021.748829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/15/2021] [Indexed: 05/25/2023]
Abstract
The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.
Collapse
Affiliation(s)
- Jessica Delfini
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Vânia Moda-Cirino
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
| | - José dos Santos Neto
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Douglas Mariani Zeffa
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Alison Fernando Nogueira
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Luriam Aparecida Brandão Ribeiro
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Paulo Maurício Ruas
- Departamento de Biologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Leandro Simões Azeredo Gonçalves
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
| |
Collapse
|
14
|
Zhang N, Lv X, Cheng X, Wang J, Liu J, Shi J, Liu J, Hu B, Chen D, Zhang G. Risk of sudden coronary death based on genetic background in Chinese Han population. Exp Ther Med 2021; 22:1068. [PMID: 34447461 PMCID: PMC8355668 DOI: 10.3892/etm.2021.10502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Associations between gene variations and sudden cardiac arrest or coronary artery disease have been reported by genome-wide association studies. However, the implication of the genetic status in cases of sudden coronary death (SCD) from the Chinese Han population has remained to be investigated. The present study established a mini-sequencing system to examine putative death-causing single nucleotide polymorphisms (SNPs) using multiplex PCR, single base extension reaction and capillary electrophoresis techniques. A total of 198 samples from the Chinese Han population (age range, 34-71 years; mean age, 53.86 years) were examined using this method. Samples were classified into three groups: Coronary heart disease (CHD, n=70), SCD (n=53) and control (n=75) group. Significant associations were identified for 10, 4 and 6 SNPs in CHD, SCD and sudden death from CHD, respectively, using the χ2 test. The SNPs obtained by binary logistic regression may be used to assess and predict the risk of disease. The predictive accuracy of the SNPs in each prediction model and their area under the receiver operating characteristic curve (AUC) values were determined. The AUC of the four SNPs (rs12429889, rs10829156, rs16942421 and rs12155623) to predict CHD was 0.928, the AUC of the six SNPs (rs2389202, rs2982694, rs10183640, rs597503, rs16942421 and rs12155623) to predict SCD was 0.922 and the AUC of the four SNPs (rs16866933, rs4621553, rs10829156 and rs12155623) to predict sudden death from CHD was 0.912. The multifactor dimensionality reduction values were as follows: 0.8690 (prediction model of CHD), 0.7601 (prediction model of SCD) and 0.7628 (prediction model of sudden death from CHD). Taken together, the results of the present study suggested that these SNPs have considerable potential for application in genetic tests to predict CHD or SCD. However, further studies are required to investigate the putative functions of these SNPs.
Collapse
Affiliation(s)
- Nenghua Zhang
- Department of Clinical Laboratory and Pathology, Municipal Key-Innovative Discipline of Molecular Diagnostics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang 314001, P.R. China
| | - Xiaochun Lv
- Department of Cardiovascular Medicine, Fenyang Hospital of Shanxi Province, Fenyang Hospital Affiliated to Shanxi Medical University, Fenyang, Shanxi 032200, P.R. China
| | - Xiaojuan Cheng
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jiaqi Wang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jinding Liu
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jie Shi
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jie Liu
- Department of Clinical Laboratory and Pathology, Municipal Key-Innovative Discipline of Molecular Diagnostics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang 314001, P.R. China
| | - Bo Hu
- Department of Clinical Laboratory and Pathology, Municipal Key-Innovative Discipline of Molecular Diagnostics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang 314001, P.R. China
| | - Deqing Chen
- Department of Pathology, Forensic and Pathology Laboratory, Judicial Expertise Center, Jiaxing University Medical College, Jiaxing, Zhejiang 314001, P.R. China
| | - Gengqian Zhang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| |
Collapse
|
15
|
de Carvalho Paulino JF, de Almeida CP, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans. J Appl Genet 2021; 62:585-600. [PMID: 34386968 DOI: 10.1007/s13353-021-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.
Collapse
Affiliation(s)
| | - Caléo Panhoca de Almeida
- Common Bean Genetic Group, Natural Center of Plant Genetics, Agronomic Institute (IAC), Campinas, SP, Brazil
| | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, USA
| | | | | | | |
Collapse
|
16
|
Elias JCF, Gonçalves-Vidigal MC, Vaz Bisneta M, Valentini G, Vidigal Filho PS, Gilio TAS, Moda-Cirino V, Song Q. Genetic Mapping for Agronomic Traits in IAPAR 81/LP97-28 Population of Common Bean ( Phaseolus vulgaris L.) under Drought Conditions. PLANTS 2021; 10:plants10081568. [PMID: 34451614 PMCID: PMC8400692 DOI: 10.3390/plants10081568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
One of the significant challenges of common bean breeding is developing cultivars with high yields under drought conditions. The present study attempted to map quantitative trait loci (QTLs) and identify molecular markers that are linked to drought tolerance in the common bean. We evaluated 160 recombinant inbred lines (RILs), derived from the cross between the carioca cultivars IAPAR 81 (drought tolerant) and LP97-28 (susceptible to drought). In 2014 and 2015, two experiments were conducted (DS-drought stress, and NS-no drought stress). In the DS experiment, water suppression was performed at the flowering stages R5 to R6. The results of our experiments showed that drought conditions play an essential role in reducing most of the traits that were evaluated. RILs under drought conditions reduced the grain yield by 62.03% and 24% in 2014 and 2015, respectively. We identified 15 quantitative trait loci distributed on the chromosomes Pv01, Pv02, Pv03, Pv07, Pv08, Pv09, Pv10, and Pv11, related to grain yield, seed yield per day, 100-seed weight, number of pods per plant, plant height, number of days for flowering, and number of days to maturity. The characteristics of seed yield per day, 100-seed weight, and number of days to maturity showed that QTLs colocalized on Pv07. Identifying QTLs that are linked to drought tolerance in the RIL population IAPAR 81 × LP97-28 is of particular importance for common bean breeding programs seeking to improve carioca beans that are cultivated in regions with drought conditions, such as Brazil.
Collapse
Affiliation(s)
- Júlio César Ferreira Elias
- Departamento de Agronomia, Universidade Estadual de Maringá—UEM, Av. Colombo 5790, Maringá 87020-900, PR, Brazil; (J.C.F.E.); (M.V.B.); (P.S.V.F.)
| | - Maria Celeste Gonçalves-Vidigal
- Departamento de Agronomia, Universidade Estadual de Maringá—UEM, Av. Colombo 5790, Maringá 87020-900, PR, Brazil; (J.C.F.E.); (M.V.B.); (P.S.V.F.)
- Correspondence:
| | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá—UEM, Av. Colombo 5790, Maringá 87020-900, PR, Brazil; (J.C.F.E.); (M.V.B.); (P.S.V.F.)
| | - Giseli Valentini
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA; (G.V.); (Q.S.)
| | - Pedro Soares Vidigal Filho
- Departamento de Agronomia, Universidade Estadual de Maringá—UEM, Av. Colombo 5790, Maringá 87020-900, PR, Brazil; (J.C.F.E.); (M.V.B.); (P.S.V.F.)
| | - Thiago Alexandre Santana Gilio
- Programa de Pós-graduação em Genética e Melhoramento de Plantas, Universidade do Estado de Mato Grosso, Cáceres 78217-900, MT, Brazil;
| | - Vânia Moda-Cirino
- Instituto Agronômico do Paraná—IAPAR, Rua Celso Garcia Cid, km 375, Londrina 86047-902, PR, Brazil;
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA; (G.V.); (Q.S.)
| |
Collapse
|
17
|
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
|