Multi-Environment Genome-Wide Association Studies of Yield Traits in Common Bean Interspecific Advanced Lines in Humid and Dry Colombian Caribbean Subregions
Assessing interspecific adaptive genetic variation across environmental gradients offers insight into the scale of habitat-dependent heritable heterotic effects, which may ultimately enable pre-breeding for abiotic stress tolerance and novel climates. However, environmentally dependent allelic effec...
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creator | López-Hernández, Felipe Burbano-Erazo, Esteban León-Pacheco, Rommel Igor Cordero-Cordero, Carina Cecilia Villanueva-Mejía, Diego F Tofiño-Rivera, Adriana Patricia Cortés, Andrés J |
description | Assessing interspecific adaptive genetic variation across environmental gradients offers insight into the scale of habitat-dependent heritable heterotic effects, which may ultimately enable pre-breeding for abiotic stress tolerance and novel climates. However, environmentally dependent allelic effects are often bypassed by intra-specific single-locality genome-wide associations studies (GWAS). Therefore, in order to bridge this gap, this study aimed at coupling an advanced panel of drought/heat susceptible common bean (Phaseolus vulgaris L.) × tolerant tepary bean (P. acutifolius A. Gray) interspecific lines with last-generation multi-environment GWAS algorithms to identify novel sources of heat and drought tolerance to the humid and dry subregions of the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme weather. A total of 87 advanced lines with interspecific ancestries were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were recorded for each genotype and inputted in modern GWAS algorithms (i.e., FarmCPU and BLINK) to identify the putative associated loci across four localities in coastal Colombia. Best-fit models revealed 47 significant quantitative trait nucleotides (QTNs) distributed in all 11 common bean chromosomes. A total of 90 flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Pathway-enriched analyses were done using the mapped output of the GWAS for each yield trait. Some genes were directly linked to the drought tolerance response; morphological, physiological, and metabolic regulation; signal transduction; and fatty acid and phospholipid metabolism. We conclude that habitat-dependent interspecific polygenic effects are likely sufficient to boost common bean adaptation to the severe climate in coastal Colombia via introgression breeding. Environmental-dependent polygenic adaptation may be due to contrasting levels of selection and the deleterious load across localities. This work offers putative associated loci for marker-assisted and genomic selection targeting the common bean's neo-tropical lowland adaptation to drought and heat. |
doi_str_mv | 10.3390/agronomy13051396 |
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However, environmentally dependent allelic effects are often bypassed by intra-specific single-locality genome-wide associations studies (GWAS). Therefore, in order to bridge this gap, this study aimed at coupling an advanced panel of drought/heat susceptible common bean (Phaseolus vulgaris L.) × tolerant tepary bean (P. acutifolius A. Gray) interspecific lines with last-generation multi-environment GWAS algorithms to identify novel sources of heat and drought tolerance to the humid and dry subregions of the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme weather. A total of 87 advanced lines with interspecific ancestries were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were recorded for each genotype and inputted in modern GWAS algorithms (i.e., FarmCPU and BLINK) to identify the putative associated loci across four localities in coastal Colombia. Best-fit models revealed 47 significant quantitative trait nucleotides (QTNs) distributed in all 11 common bean chromosomes. A total of 90 flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Pathway-enriched analyses were done using the mapped output of the GWAS for each yield trait. Some genes were directly linked to the drought tolerance response; morphological, physiological, and metabolic regulation; signal transduction; and fatty acid and phospholipid metabolism. We conclude that habitat-dependent interspecific polygenic effects are likely sufficient to boost common bean adaptation to the severe climate in coastal Colombia via introgression breeding. Environmental-dependent polygenic adaptation may be due to contrasting levels of selection and the deleterious load across localities. This work offers putative associated loci for marker-assisted and genomic selection targeting the common bean's neo-tropical lowland adaptation to drought and heat.</description><identifier>ISSN: 2073-4395</identifier><identifier>EISSN: 2073-4395</identifier><identifier>DOI: 10.3390/agronomy13051396</identifier><language>eng</language><publisher>MDPI AG</publisher><subject>Analysis ; Beans ; Chromosomes ; Fatty acids ; Genetic research ; Genomes ; Genomics ; Legumes ; Mimosaceae ; Physiological aspects ; Single nucleotide polymorphisms</subject><ispartof>Agronomy (Basel), 2023-05, Vol.13 (5)</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,865,27929,27930</link.rule.ids></links><search><creatorcontrib>López-Hernández, Felipe</creatorcontrib><creatorcontrib>Burbano-Erazo, Esteban</creatorcontrib><creatorcontrib>León-Pacheco, Rommel Igor</creatorcontrib><creatorcontrib>Cordero-Cordero, Carina Cecilia</creatorcontrib><creatorcontrib>Villanueva-Mejía, Diego F</creatorcontrib><creatorcontrib>Tofiño-Rivera, Adriana Patricia</creatorcontrib><creatorcontrib>Cortés, Andrés J</creatorcontrib><title>Multi-Environment Genome-Wide Association Studies of Yield Traits in Common Bean Interspecific Advanced Lines in Humid and Dry Colombian Caribbean Subregions</title><title>Agronomy (Basel)</title><description>Assessing interspecific adaptive genetic variation across environmental gradients offers insight into the scale of habitat-dependent heritable heterotic effects, which may ultimately enable pre-breeding for abiotic stress tolerance and novel climates. However, environmentally dependent allelic effects are often bypassed by intra-specific single-locality genome-wide associations studies (GWAS). Therefore, in order to bridge this gap, this study aimed at coupling an advanced panel of drought/heat susceptible common bean (Phaseolus vulgaris L.) × tolerant tepary bean (P. acutifolius A. Gray) interspecific lines with last-generation multi-environment GWAS algorithms to identify novel sources of heat and drought tolerance to the humid and dry subregions of the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme weather. A total of 87 advanced lines with interspecific ancestries were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were recorded for each genotype and inputted in modern GWAS algorithms (i.e., FarmCPU and BLINK) to identify the putative associated loci across four localities in coastal Colombia. Best-fit models revealed 47 significant quantitative trait nucleotides (QTNs) distributed in all 11 common bean chromosomes. A total of 90 flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Pathway-enriched analyses were done using the mapped output of the GWAS for each yield trait. Some genes were directly linked to the drought tolerance response; morphological, physiological, and metabolic regulation; signal transduction; and fatty acid and phospholipid metabolism. We conclude that habitat-dependent interspecific polygenic effects are likely sufficient to boost common bean adaptation to the severe climate in coastal Colombia via introgression breeding. Environmental-dependent polygenic adaptation may be due to contrasting levels of selection and the deleterious load across localities. This work offers putative associated loci for marker-assisted and genomic selection targeting the common bean's neo-tropical lowland adaptation to drought and heat.</description><subject>Analysis</subject><subject>Beans</subject><subject>Chromosomes</subject><subject>Fatty acids</subject><subject>Genetic research</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Legumes</subject><subject>Mimosaceae</subject><subject>Physiological aspects</subject><subject>Single nucleotide polymorphisms</subject><issn>2073-4395</issn><issn>2073-4395</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid/><recordid>eNptjT1rwzAQhk1poSHN3lHQ2alkxZI9um6aBFI6JFA6BVk6myu2VCw7kB_T_1r1Y8jQu-GO43mfi6JbRuec5_ReNb2zrjsxTlPGc3ERTRIqebzgeXp5tl9HM-_faaic8YzKSfT5PLYDxkt7xKDowA5kBUEF8SsaIIX3TqMa0FmyG0aD4ImryRtCa8i-Vzh4gpaUrusC8QDKko0doPcfoLFGTQpzVFaDIVu08MOuxw4NUdaQx_4Ukq3rKgy5UvVYVd-G3Vj10ISX_ia6qlXrYfY3p9H-abkv1_H2ZbUpi23cCJnHSSoT4IwBFTmXTAmaSpYwvdB5AkIJJjMwSZLQOluklTCqrjJDqRZVLYUEzqfR3a-2US0c0NZu6JXu0OtDIVOaZUKwPFDzf6jQBjrUzkKN4X4W-AK2K32C</recordid><startdate>20230501</startdate><enddate>20230501</enddate><creator>López-Hernández, Felipe</creator><creator>Burbano-Erazo, Esteban</creator><creator>León-Pacheco, Rommel Igor</creator><creator>Cordero-Cordero, Carina Cecilia</creator><creator>Villanueva-Mejía, Diego F</creator><creator>Tofiño-Rivera, Adriana Patricia</creator><creator>Cortés, Andrés J</creator><general>MDPI AG</general><scope/></search><sort><creationdate>20230501</creationdate><title>Multi-Environment Genome-Wide Association Studies of Yield Traits in Common Bean Interspecific Advanced Lines in Humid and Dry Colombian Caribbean Subregions</title><author>López-Hernández, Felipe ; Burbano-Erazo, Esteban ; León-Pacheco, Rommel Igor ; Cordero-Cordero, Carina Cecilia ; Villanueva-Mejía, Diego F ; Tofiño-Rivera, Adriana Patricia ; Cortés, Andrés J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-g679-2572e311e069371a6057121c4c92e6a6178ed2220f845b6dafb8d00c6bf767e33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Beans</topic><topic>Chromosomes</topic><topic>Fatty acids</topic><topic>Genetic research</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Legumes</topic><topic>Mimosaceae</topic><topic>Physiological aspects</topic><topic>Single nucleotide polymorphisms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>López-Hernández, Felipe</creatorcontrib><creatorcontrib>Burbano-Erazo, Esteban</creatorcontrib><creatorcontrib>León-Pacheco, Rommel Igor</creatorcontrib><creatorcontrib>Cordero-Cordero, Carina Cecilia</creatorcontrib><creatorcontrib>Villanueva-Mejía, Diego F</creatorcontrib><creatorcontrib>Tofiño-Rivera, Adriana Patricia</creatorcontrib><creatorcontrib>Cortés, Andrés J</creatorcontrib><jtitle>Agronomy (Basel)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>López-Hernández, Felipe</au><au>Burbano-Erazo, Esteban</au><au>León-Pacheco, Rommel Igor</au><au>Cordero-Cordero, Carina Cecilia</au><au>Villanueva-Mejía, Diego F</au><au>Tofiño-Rivera, Adriana Patricia</au><au>Cortés, Andrés J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multi-Environment Genome-Wide Association Studies of Yield Traits in Common Bean Interspecific Advanced Lines in Humid and Dry Colombian Caribbean Subregions</atitle><jtitle>Agronomy (Basel)</jtitle><date>2023-05-01</date><risdate>2023</risdate><volume>13</volume><issue>5</issue><issn>2073-4395</issn><eissn>2073-4395</eissn><abstract>Assessing interspecific adaptive genetic variation across environmental gradients offers insight into the scale of habitat-dependent heritable heterotic effects, which may ultimately enable pre-breeding for abiotic stress tolerance and novel climates. However, environmentally dependent allelic effects are often bypassed by intra-specific single-locality genome-wide associations studies (GWAS). Therefore, in order to bridge this gap, this study aimed at coupling an advanced panel of drought/heat susceptible common bean (Phaseolus vulgaris L.) × tolerant tepary bean (P. acutifolius A. Gray) interspecific lines with last-generation multi-environment GWAS algorithms to identify novel sources of heat and drought tolerance to the humid and dry subregions of the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme weather. A total of 87 advanced lines with interspecific ancestries were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were recorded for each genotype and inputted in modern GWAS algorithms (i.e., FarmCPU and BLINK) to identify the putative associated loci across four localities in coastal Colombia. Best-fit models revealed 47 significant quantitative trait nucleotides (QTNs) distributed in all 11 common bean chromosomes. A total of 90 flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Pathway-enriched analyses were done using the mapped output of the GWAS for each yield trait. Some genes were directly linked to the drought tolerance response; morphological, physiological, and metabolic regulation; signal transduction; and fatty acid and phospholipid metabolism. We conclude that habitat-dependent interspecific polygenic effects are likely sufficient to boost common bean adaptation to the severe climate in coastal Colombia via introgression breeding. Environmental-dependent polygenic adaptation may be due to contrasting levels of selection and the deleterious load across localities. This work offers putative associated loci for marker-assisted and genomic selection targeting the common bean's neo-tropical lowland adaptation to drought and heat.</abstract><pub>MDPI AG</pub><doi>10.3390/agronomy13051396</doi></addata></record> |
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subjects | Analysis Beans Chromosomes Fatty acids Genetic research Genomes Genomics Legumes Mimosaceae Physiological aspects Single nucleotide polymorphisms |
title | Multi-Environment Genome-Wide Association Studies of Yield Traits in Common Bean Interspecific Advanced Lines in Humid and Dry Colombian Caribbean Subregions |
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