Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat
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ORIGINAL ARTICLE
Genome‑wide association analysis of stem water‑soluble carbohydrate content in bread wheat Luping Fu1 · Jingchun Wu1 · Shurong Yang2 · Yirong Jin3 · Jindong Liu4 · Mengjiao Yang1 · Awais Rasheed1,5 · Yong Zhang1 · Xianchun Xia1 · Ruilian Jing1 · Zhonghu He1,6 · Yonggui Xiao1 Received: 22 January 2020 / Accepted: 19 June 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated. Abstract Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genomewide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding. Abbreviations BLUE Best linear unbiased estimation FarmCPU Fixed and random model circulating probability unification Communicated by Jessica Rutkoski. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03640-x) contains supplementary material, which is available to authorized users.
GWAS Genome-wide association study GY Grain yield H2 Broad-sense heritability KASP Kompetitive allele-specific PCR LD Linkage disequilibrium MAF Minor allele frequency MAS Marker-assisted selection MTA Marker-trait association NIRS Near-infrared spectroscopy
* Zhonghu He [email protected]
3
Dezhou Institute of Agricultural Sciences, Dezhou 253000, Shandong, China
* Yonggui Xiao [email protected]
4
A
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