Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress
Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this w...
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Frontiers Media S.A.
2020-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2020.574674/full |
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| author | Paula Arielle Mendes Ribeiro Valdisser Paula Arielle Mendes Ribeiro Valdisser Bárbara S. F. Müller Janeo Eustáquio de Almeida Filho Odilon Peixoto Morais Júnior Cléber Morais Guimarães Tereza C. O. Borba Isabela Pavanelli de Souza Isabela Pavanelli de Souza Maria Imaculada Zucchi Maria Imaculada Zucchi Leandro G. Neves Alexandre S. G. Coelho Claudio Brondani Rosana Pereira Vianello |
| author_facet | Paula Arielle Mendes Ribeiro Valdisser Paula Arielle Mendes Ribeiro Valdisser Bárbara S. F. Müller Janeo Eustáquio de Almeida Filho Odilon Peixoto Morais Júnior Cléber Morais Guimarães Tereza C. O. Borba Isabela Pavanelli de Souza Isabela Pavanelli de Souza Maria Imaculada Zucchi Maria Imaculada Zucchi Leandro G. Neves Alexandre S. G. Coelho Claudio Brondani Rosana Pereira Vianello |
| author_sort | Paula Arielle Mendes Ribeiro Valdisser |
| collection | DOAJ |
| description | Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r2sv), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean. |
| first_indexed | 2024-12-23T23:24:44Z |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-b7271720552f4b61832dc8c72eb9522f2022-12-21T17:26:14ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-11-011110.3389/fpls.2020.574674574674Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought StressPaula Arielle Mendes Ribeiro Valdisser0Paula Arielle Mendes Ribeiro Valdisser1Bárbara S. F. Müller2Janeo Eustáquio de Almeida Filho3Odilon Peixoto Morais Júnior4Cléber Morais Guimarães5Tereza C. O. Borba6Isabela Pavanelli de Souza7Isabela Pavanelli de Souza8Maria Imaculada Zucchi9Maria Imaculada Zucchi10Leandro G. Neves11Alexandre S. G. Coelho12Claudio Brondani13Rosana Pereira Vianello14Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, BrazilGenetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, BrazilDepartment of Horticultural Sciences, University of Florida, Gainesville, FL, United StatesBayer Brazil – Crop Science, Coxilha, BrazilDepartment of Genetics and Plant Breeding, School of Agronomy, Federal University of Goiás, Goiânia, BrazilPlant Physiology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, BrazilBiotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, BrazilBiotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, BrazilPostgraduate Program in Biological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, BrazilGenetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, BrazilAgribusiness Technology Agency of São Paulo State, Agriculture and Food Supply Secretary of São Paulo, Piracicaba, BrazilRapid Genomics, Gainesville, FL, United States0School of Agronomy, Federal University of Goiás, Goiânia, BrazilBiotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, BrazilBiotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, BrazilDrought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r2sv), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.https://www.frontiersin.org/articles/10.3389/fpls.2020.574674/fullPhaseolus vulgarisDArTseq markersCaptureSeqgenetic diversityseed-weightyield |
| spellingShingle | Paula Arielle Mendes Ribeiro Valdisser Paula Arielle Mendes Ribeiro Valdisser Bárbara S. F. Müller Janeo Eustáquio de Almeida Filho Odilon Peixoto Morais Júnior Cléber Morais Guimarães Tereza C. O. Borba Isabela Pavanelli de Souza Isabela Pavanelli de Souza Maria Imaculada Zucchi Maria Imaculada Zucchi Leandro G. Neves Alexandre S. G. Coelho Claudio Brondani Rosana Pereira Vianello Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress Frontiers in Plant Science Phaseolus vulgaris DArTseq markers CaptureSeq genetic diversity seed-weight yield |
| title | Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress |
| title_full | Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress |
| title_fullStr | Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress |
| title_full_unstemmed | Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress |
| title_short | Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress |
| title_sort | genome wide association studies detect multiple qtls for productivity in mesoamerican diversity panel of common bean under drought stress |
| topic | Phaseolus vulgaris DArTseq markers CaptureSeq genetic diversity seed-weight yield |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2020.574674/full |
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