Genome-wide association study for pre-harvest sprouting resistance in a large germplasm collection of Chinese wheat landraces

Zhou, Yong, Tang, Hao, Cheng, Meng-Ping, Dankwa, Kwame O., Chen, Zhong-Xu, Li, Zhan-Yi, Gao, Shang, Liu, Ya-Xi, Jiang, Qian-Tao, Lan, Xiu-Jin, Pu, Zhi-En, Wei, Yu-Ming, Zheng, You-Liang, Hickey, Lee T. and Wang, Ji-Rui (2017) Genome-wide association study for pre-harvest sprouting resistance in a large germplasm collection of Chinese wheat landraces. Frontiers in Plant Science, 8 . doi:10.3389/fpls.2017.00401


Author Zhou, Yong
Tang, Hao
Cheng, Meng-Ping
Dankwa, Kwame O.
Chen, Zhong-Xu
Li, Zhan-Yi
Gao, Shang
Liu, Ya-Xi
Jiang, Qian-Tao
Lan, Xiu-Jin
Pu, Zhi-En
Wei, Yu-Ming
Zheng, You-Liang
Hickey, Lee T.
Wang, Ji-Rui
Title Genome-wide association study for pre-harvest sprouting resistance in a large germplasm collection of Chinese wheat landraces
Journal name Frontiers in Plant Science   Check publisher's open access policy
ISSN 1664-462X
Publication date 2017-04-06
Sub-type Article (original research)
DOI 10.3389/fpls.2017.00401
Open Access Status DOI
Volume 8
Total pages 13
Place of publication Lausanne, Switzerland
Publisher Frontiers Research Foundation
Language eng
Subject 1110 Plant Science
Abstract Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7-79.6%) compared to red-grained accessions (19.1-56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.
Formatted abstract
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7-79.6%) compared to red-grained accessions (19.1-56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R2 = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.
Keyword Wheat
Landrace
Pre-harvest sprouting
Gwas
Haplotypes
Geographic distribution
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID 31171555
31571654
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
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