Genetic mapping of a major QTL promoting homoeologous chromosome pairing in a wheat landrace

https://doi.org/10.1007/s00122-019-03344-x

Chaolan Fan, Jiangtao Luo, Shujie Zhang, Meng Liu, Qingcheng Li, Yazhou Li, Lei Huang, Xuejiao Chen, Shunzong Ning, Zhongwei Yuan, Lianquan Zhang, Jirui Wang, Youliang Zheng, Dengcai Liu,Ming Hao

Abstract

Polyhaploid hybrids of a Chinese common wheat landrace Kaixian-luohanmai (KL) and related species show increased levels of chromosome pairing. Over 90% of that pairing is between homoeologous arms of wheat chromosomes, with a very strong preference for pairing between homoeologs from genomes A and D. Wheat–rye pairing was also observed at low frequency. Two mapping populations were created from the hybrids of KL with two wheat genotypes top crossed to rye. Mean chiasmata numbers per plant were used as phenotypic data. Wheat 660 K and 15 K SNP arrays, DArT markers and SSR markers were used for genotyping of the top-cross ABDR hybrids. One major QTL, named QPh.sicau-3A, for increased homoeologous pairing was detected on chromosome arm 3AL, and it was responsible for ca. 16% of the total variation. This QTL was located in the interval 696–725 Mb in the Chinese Spring reference genome. SNP markers closely linked with QPh.sicau-3A were converted to KASP markers and validated for marker-assisted selection.