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. 2020 Oct 27;20(1):491.
doi: 10.1186/s12870-020-02693-w.

Genome-wide association analysis of stripe rust resistance in modern Chinese wheat

Mengjie Jia  1   2 , Lijun Yang  3 , Wei Zhang  4 , Garry Rosewarne  5   6 , Junhui Li  1 , Enian Yang  7 , Ling Chen  1 , Wenxue Wang  1 , Yike Liu  1 , Hanwen Tong  1 , Weijie He  1 , Yuqing Zhang  1 , Zhanwang Zhu  8 , Chunbao Gao  9   10
Affiliations

Genome-wide association analysis of stripe rust resistance in modern Chinese wheat

Mengjie Jia et al. BMC Plant Biol. .

Abstract

Background: Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm.

Results: Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation.

Conclusion: The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.

Keywords: Marker-trait association; Single nucleotide polymorphism (SNP); Triticum aestivum; Yellow rust.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The pearson correlation coefficients of stripe rust severity in the natural populaiton among five environments
Fig. 2
Fig. 2
Sample numbers and averaged stripe rust severity of wheat accessions from different provinces of China. BJ, Beijing, 52.43%; HE, Hebei, 51.96%; SD, Shandong, 57.54%; SX, Shanxi, 51.04%; SN, Shaanxi, 35.38%; NX, Ningxia, 68.39%; GS, Gansu, 19.95%; JS, Jiangsu, 59.47%; AH, Anhui, 49.45%; HA, Henan, 55.06%; HB, Hubei, 49.86%; SC, Sichuan, 37.00%. Numeral in each province represents the number of cultivars (lines) sampled. Different colors represent corresponding stripe rust severity according to the legend. Map of China was obtained from http://bzdt.ch.mnr.gov.cn
Fig. 3
Fig. 3
Manhattan plots for stripe rust severity of 240 wheat accessions performed by the mixed linear model with Tassel. The horizontal line indicates the threshold for significance
Fig. 4
Fig. 4
Manhattan plots for stripe rust severity of 240 wheat accessions performed by the mixed linear model with GAPIT. The horizontal line indicates the threshold for significance
Fig. 5
Fig. 5
Allelic frequencies of the 12 stable QTLs in wheat cultivars from different provinces in China and CIMMYT lines. Provinces with number of wheat cultivars less than 9 were not shown
Fig. 6
Fig. 6
Averaged stripe rust maximum disease severity of lines with different number of favorable alleles of mapped QTLs. Arabic numerals on the bars indicates the number of accessions corresponding to each class
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