Identification and validation of a major QTL for kernel length in bread wheat based on two F3 biparental populations

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08608-3

BMC Genomics，23，386 (2022)

Xinlin Xie, Shuiqin Li, Hang Liu, Qiang Xu, Huaping Tang, Yang Mu, Mei Deng, Qiantao Jiang, Guoyue Chen, Pengfei Qi, Wei Li, Zhien Pu, Ahsan Habib, Yuming Wei, Youliang Zheng, Xiujin Lan & Jian Ma

Background

High yield and quality are essential goals of wheat (Triticum aestivumL.) breeding. Kernel length (KL), as a main component of kernel size, can indirectly change kernel weight and then affects yield. Identification and utilization of excellent loci in wheat genetic resources is of great significance for cultivating high yield and quality wheat. Genetic identification of loci for KL has been performed mainly through genome-wide association study in natural populations or QTL mapping based on genetic linkage map in high generation populations.

Results

In this study, an F₃biparental population derived from the cross between an EMS mutant BLS1 selected from an EMS-induced wheat genotype LJ2135 (derived from the hybrid progeny of a spelt wheat (T.speltaL.) and a common wheat) mutant bank and a local breeding line 99E18 was used to rapidly identify loci controlling KL based on Bulked Segregant Analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array. The highest ratio of polymorphic SNPs was located on chromosome 4A. Linkage map analysis showed that 33 Kompetitive Allele Specific PCR markers were linked to the QTL for KL (Qkl.sicau-BLE18-4A) identified in three environments as well as the best linear unbiased prediction (BLUP) dataset. This QTL explained 10.87—19.30% of the phenotypic variation. Its effect was successfully confirmed in another F₃population with the two flanking markersKASP-AX-111536305andKASP-AX-110174441. Compared with previous studies and given that the of BLS1 has the genetic background of spelt wheat, the major QTL was likely a new one. A few of predicted genes related to regulation of kernel development were identified in the interval of the detected QTL.

Conclusion

A major, novel and stable QTL (Qkl.sicau-BLE18-4A) for KL was identified and verified in two F₃biparental populations across three environments. Significant relationships among KL, kernel width (KW) and thousand kernel weight (TKW) were identified. Four predicted genes related to kernel growth regulation were detected in the interval ofQkl.sicau-BLE18-4A. Furthermore, this study laid foundation on subsequent fine mapping work and provided a possibility for breeding of elite wheat varieties.