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Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population
Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underl...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9652842/ https://www.ncbi.nlm.nih.gov/pubmed/36368932 http://dx.doi.org/10.1186/s12864-022-08970-2 |
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author | Yang, Guang Li, Wei Fan, Chao Liu, Miao Liu, Jianxin Liang, Wenwei Wang, Ling Di, Shufeng Fang, Chao Li, Haiyang Ding, Guohua Bi, Yingdong Lai, Yongcai |
author_facet | Yang, Guang Li, Wei Fan, Chao Liu, Miao Liu, Jianxin Liang, Wenwei Wang, Ling Di, Shufeng Fang, Chao Li, Haiyang Ding, Guohua Bi, Yingdong Lai, Yongcai |
author_sort | Yang, Guang |
collection | PubMed |
description | Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log(10)(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08970-2. |
format | Online Article Text |
id | pubmed-9652842 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-96528422022-11-15 Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population Yang, Guang Li, Wei Fan, Chao Liu, Miao Liu, Jianxin Liang, Wenwei Wang, Ling Di, Shufeng Fang, Chao Li, Haiyang Ding, Guohua Bi, Yingdong Lai, Yongcai BMC Genomics Research Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log(10)(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08970-2. BioMed Central 2022-11-11 /pmc/articles/PMC9652842/ /pubmed/36368932 http://dx.doi.org/10.1186/s12864-022-08970-2 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Yang, Guang Li, Wei Fan, Chao Liu, Miao Liu, Jianxin Liang, Wenwei Wang, Ling Di, Shufeng Fang, Chao Li, Haiyang Ding, Guohua Bi, Yingdong Lai, Yongcai Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
title | Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
title_full | Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
title_fullStr | Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
title_full_unstemmed | Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
title_short | Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
title_sort | genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9652842/ https://www.ncbi.nlm.nih.gov/pubmed/36368932 http://dx.doi.org/10.1186/s12864-022-08970-2 |
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