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

Zhi-peng ZHANG; Zhen LI; Fang HE; Ji-juan LÜ; Bin XIE; Xiao-yu YI; Jia-min LI; Jing LI; Jing-han SONG; Zhi-en PU; Jian MA; Yuan-ying PENG; Guo-yue CHEN; Yu-ming WEI; You-liang ZHENG; Wei LI

Journal of Integrative Agriculture (Nov 2023)

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

Zhi-peng ZHANG,
Zhen LI,
Fang HE,
Ji-juan LÜ,
Bin XIE,
Xiao-yu YI,
Jia-min LI,
Jing LI,
Jing-han SONG,
Zhi-en PU,
Jian MA,
Yuan-ying PENG,
Guo-yue CHEN,
Yu-ming WEI,
You-liang ZHENG,
Wei LI

Affiliations

Zhi-peng ZHANG: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China; Huaiyin Institute of Agricultural Sciences of Xuhuai Area in Jiangsu, Huai'an 223001, P.R.China
Zhen LI: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Fang HE: Sichuan Provincial Seed Station, Chengdu 610044, P.R.China
Ji-juan LÜ: Sichuan Provincial Seed Station, Chengdu 610044, P.R.China
Bin XIE: Sichuan Provincial Seed Station, Chengdu 610044, P.R.China
Xiao-yu YI: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Jia-min LI: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Jing LI: Huaiyin Institute of Agricultural Sciences of Xuhuai Area in Jiangsu, Huai'an 223001, P.R.China
Jing-han SONG: Beijing Foreign Studies University, Beijing 100081, P.R.China
Zhi-en PU: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China
Jian MA: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Yuan-ying PENG: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Guo-yue CHEN: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Yu-ming WEI: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
You-liang ZHENG: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
Wei LI: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China; Correspondence LI Wei, Tel/Fax: +86-28-82650350

Journal volume & issue: Vol. 22, no. 11
pp. 3380 – 3393

Abstract

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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.

Published in Journal of Integrative Agriculture

ISSN: 2095-3119 (Print); 2352-3425 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Agriculture: Agriculture (General)
Website: https://www.journals.elsevier.com/journal-of-integrative-agriculture

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