通过全基因组关联定位揭示四川小麦重要农艺性状的遗传位点和候选基因

doi:10.1016/j.jia.2023.02.030

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (11): 3380-3393.DOI: 10.1016/j.jia.2023.02.030

通过全基因组关联定位揭示四川小麦重要农艺性状的遗传位点和候选基因

收稿日期:2022-11-05 接受日期:2022-12-27 出版日期:2023-11-20 发布日期:2023-11-09

Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat

ZHANG Zhi-peng^{1, 2, 3, 5*}, LI Zhen^{1, 2, 3*}, HE Fang^4*, LÜ Ji-juan⁴, XIE Bin⁴, YI Xiao-yu^{1, 2, 3}, LI Jia-min^{1, 2, 3}, LI Jing⁵, SONG Jing-han⁶, PU Zhi-en^{1, 2}, MA Jian^{1, 3}, PENG Yuan-ying^{1, 3}, CHEN Guo-yue^{1, 3}, WEI Yu-ming^{1, 3}, ZHENG You-liang^{1, 3}, LI Wei^{1, 2, 3#}

¹ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China
² College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China
³ Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
⁴ Sichuan Provincial Seed Station, Chengdu 610044, P.R.China
⁵Huaiyin Institute of Agricultural Sciences of Xuhuai Area in Jiangsu, Huai’an 223001, P.R.China
⁶ Beijing Foreign Studies University, Beijing 100081, P.R.China

Received:2022-11-05 Accepted:2022-12-27 Online:2023-11-20 Published:2023-11-09
About author:#Correspondence LI Wei, Tel/Fax: +86-28-82650350, E-mail: liw03@163.com * The authors have contributed equally to this paper.
Supported by:
This work was supported by the Sichuan Science and Technology Program, China (2022ZDZX0014 and 2021YFYZ0002) and the Plan of Tianfu Qingcheng of Sichuan Province, China.

摘要/Abstract

摘要：

提高小麦产量是全球小麦育种者的长期目标。发掘优良遗传资源，解析小麦重要农艺性状的遗传基础，是小麦高产育种的必经之路。本研究评价了两年七个环境中由156个育成品种和77个地方品种组成的四川小麦自然群体的9个重要农艺性状表现。农艺性状调查结果表明，地方品种分蘖较多，穗粒数（KNS）较高，育成品种千粒重（TKW）和穗粒重（KWS）较高。9个农艺性状的广义遗传力（H ²）在0.74到0.95之间。利用来自小麦55K SNP芯片的43198个单核苷酸多态性（SNP）标记进行群体结构分析可以将自然群体分为三组。基于混合线性模型Q+K方法的全基因组关联分析（GWAS）共鉴定出67个数量性状位点（QTL）。本研究主要对三个重要性状的QTL进行了分析，即分别检测到的可育分蘖数（FTN）位点QFTN.sicau-7BL.1的四种单倍型、KNS位点QKNS.sicau-1AL.2的三种单倍型和TKW位点QTKW.sicau-3BS.1的四种单倍型。从2002—2013年区域试验的42个品种的产量表现来看，FTN-Hap2、KNS-Hap1和TKW-Hap2分别是每个QTL中的优良单倍型。具有三个优良单倍型的品种相比具有两个或一个优良单倍型的品种产量更高。此外，基于每穗粒数的QTL位点 QKNS.sicau-1AL.2开发了连锁的KASP-AX-108866053标记能在2018年至2021年区域试验中鉴定63个品种的三种单倍型（或等位基因）。这些遗传位点和连锁标记可用于标记辅助选择或基于图谱的基因克隆，用于小麦产量的遗传改良。

Abstract:

Increasing wheat yield is a long-term goal for wheat breeders around the world. Exploiting elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for high-yield wheat breeding. This study evaluated nine crucial agronomic traits found in a natural population of 156 wheat varieties and 77 landraces from Sichuan, China in seven environments over two years. The results of this investigation of agronomic traits showed that the landraces had more tillers and higher kernel numbers per spike (KNS), while the breeding varieties had higher thousand-kernel weight (TKW) and kernel weight per spike (KWS). The generalized heritability (H²) values of the nine agronomic traits varied from 0.74 to 0.95. Structure analysis suggested that the natural population could be divided into three groups using 43 198 single nucleotide polymorphism (SNP) markers from the wheat 55K SNP chip. A total of 67 quantitative trait loci (QTLs) were identified by the genome-wide association study (GWAS) analysis based on the Q+K method of a mixed linear model. Three important QTLs were analyzed in this study. Four haplotypes of QFTN.sicau-7BL.1 for fertile tillers number (FTN), three haplotypes of QKNS.sicau-1AL.2 for KNS, and four haplotypes of QTKW.sicau-3BS.1 for TKW were detected. FTN-Hap2, KNS-Hap1, and TKW-Hap2 were excellent haplotypes for each QTL based on the yield performance of 42 varieties in regional trials from 2002 to 2013. The varieties with all three haplotypes showed the highest yield compared to those with either two haplotypes or one haplotype. In addition, the KASP-AX-108866053 marker of QTL QKNS.sicau-1AL.2 was successfully distinguished between three haplotypes (or alleles) in 63 varieties based on the number of kernels per spike in regional trials between 2018 and 2021. These genetic loci and reliable makers can be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of wheat yield.

Key words: Sichuan wheat , GWAS , yield traits , haplotype analysis , KASP

ZHANG Zhi-peng, LI Zhen, HE Fang, LÜ Ji-juan, XIE Bin, YI Xiao-yu, LI Jia-min, LI Jing, SONG Jing-han, PU Zhi-en, MA Jian, PENG Yuan-ying, CHEN Guo-yue, WEI Yu-ming, ZHENG You-liang, LI Wei. 通过全基因组关联定位揭示四川小麦重要农艺性状的遗传位点和候选基因[J]. Journal of Integrative Agriculture, 2023, 22(11): 3380-3393.

ZHANG Zhi-peng, LI Zhen, HE Fang, LÜ Ji-juan, XIE Bin, YI Xiao-yu, LI Jia-min, LI Jing, SONG Jing-han, PU Zhi-en, MA Jian, PENG Yuan-ying, CHEN Guo-yue, WEI Yu-ming, ZHENG You-liang, LI Wei. Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat[J]. Journal of Integrative Agriculture, 2023, 22(11): 3380-3393.

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通过全基因组关联定位揭示四川小麦重要农艺性状的遗传位点和候选基因

Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat

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