Rapid mapping of a chlorina mutant gene cn-A1 in hexaploid wheat by bulked segregant analysis and single nucleotide polymorphism genotyping arrays

Abstract

The yellow–green leaf mutant can be exploited in photosynthesis and plant development research. A Triticum aestivum mutant with the chlorina phenotype, here called B23, was produced by treatment with the chemical mutagen sodium azide. This B23 mutant showed significantly lower chlorophyll content than wild-type Saannong33, and its chloroplast structure was abnormal. All its yield-related traits, except for the number of spikes per plant, were also significantly decreased. Genetic analysis confirmed that the mutant phenotype was controlled by a recessive gene, here designated cn-A1. Using bulked segregant analysis and the wheat 660K single nucleotide polymorphism array, the cn-A1 gene was mapped to chromosome 7AL, and 11 polymorphic markers were developed. Further analysis showed that cn-A1 was located in a 1.1-cM genetic region flanked by Kompetitive allele specific PCR (KASP) markers 660K-7A12 and 660K-7A20, which corresponded to a physical interval of 3.48 Mb in T. aestivum cv. Chinese Spring chromosome 7AL containing 47 predicted genes with high confidence. These results are expected to accelerate the process of cloning the cn-A1 gene and facilitate understanding of the mechanisms underlying chlorophyll metabolism and chloroplast development in wheat.