Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

Abstract Background Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultiva...

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Autores principales:	Caijing Li, Jindong Liu, Jianxin Bian, Tao Jin, Baoli Zou, Shilei Liu, Xiangyu Zhang, Peng Wang, Jingai Tan, Guangliang Wu, Qin Chen, Yanning Wang, Qi Zhong, Shiying Huang, Mengmeng Yang, Tao Huang, Haohua He, Jianmin Bian
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Cold tolerance Rice landraces GWAS Seedling survival rate (SR) QTL Botany QK1-989
Acceso en línea:	https://doaj.org/article/3851360903fb451887996483553d596f
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spelling	oai:doaj.org-article:3851360903fb451887996483553d596f2021-11-21T12:05:41ZIdentification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS10.1186/s12870-021-03317-71471-2229https://doaj.org/article/3851360903fb451887996483553d596f2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03317-7https://doaj.org/toc/1471-2229Abstract Background Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage. Results In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2–2, qSR3–1, qSR3–2, qSR3–3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2–1, qSR3–4, qSR3–5, qSR3–6, qSR3–7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9. Conclusion This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.Caijing LiJindong LiuJianxin BianTao JinBaoli ZouShilei LiuXiangyu ZhangPeng WangJingai TanGuangliang WuQin ChenYanning WangQi ZhongShiying HuangMengmeng YangTao HuangHaohua HeJianmin BianBMCarticleCold toleranceRice landracesGWASSeedling survival rate (SR)QTLBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Cold tolerance Rice landraces GWAS Seedling survival rate (SR) QTL Botany QK1-989
spellingShingle	Cold tolerance Rice landraces GWAS Seedling survival rate (SR) QTL Botany QK1-989 Caijing Li Jindong Liu Jianxin Bian Tao Jin Baoli Zou Shilei Liu Xiangyu Zhang Peng Wang Jingai Tan Guangliang Wu Qin Chen Yanning Wang Qi Zhong Shiying Huang Mengmeng Yang Tao Huang Haohua He Jianmin Bian Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
description	Abstract Background Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage. Results In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2–2, qSR3–1, qSR3–2, qSR3–3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2–1, qSR3–4, qSR3–5, qSR3–6, qSR3–7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9. Conclusion This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.
format	article
author	Caijing Li Jindong Liu Jianxin Bian Tao Jin Baoli Zou Shilei Liu Xiangyu Zhang Peng Wang Jingai Tan Guangliang Wu Qin Chen Yanning Wang Qi Zhong Shiying Huang Mengmeng Yang Tao Huang Haohua He Jianmin Bian
author_facet	Caijing Li Jindong Liu Jianxin Bian Tao Jin Baoli Zou Shilei Liu Xiangyu Zhang Peng Wang Jingai Tan Guangliang Wu Qin Chen Yanning Wang Qi Zhong Shiying Huang Mengmeng Yang Tao Huang Haohua He Jianmin Bian
author_sort	Caijing Li
title	Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
title_short	Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
title_full	Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
title_fullStr	Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
title_full_unstemmed	Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
title_sort	identification of cold tolerance qtls at the bud burst stage in 211 rice landraces by gwas
publisher	BMC
publishDate	2021
url	https://doaj.org/article/3851360903fb451887996483553d596f
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Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

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