Combining SNP genotyping array with bulked segregant analysis to map a gene controlling adult-plant resistance to stripe rust in wheat line 03031-1-5 H62

Authors: WU, JIANJUI - Northwest Agriculture And Forestry University; WANG, QILIN - Northwest Agriculture And Forestry University; XU, LIANGSHENG - Northwest Agriculture And Forestry University; Chen, Xianming; LI, BEI - Northwest Agriculture And Forestry University; MU, JINGMEI - Northwest Agriculture And Forestry University; ZEN, QINGDONG - Northwest Agriculture And Forestry University; HUANG, LILI - Northwest Agriculture And Forestry University; HAN, DEJUN - Northwest Agriculture And Forestry University; KANG, ZHENSHENG - Northwest Agriculture And Forestry University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2017
Publication Date: 1/20/2018
Citation: Wu, J., Wang, Q., Xu, L., Chen, X., Li, B., Mu, J., Zen, Q., Huang, L., Han, D., Kang, Z. 2018. Combining SNP genotyping array with bulked segregant analysis to map a gene controlling adult-plant resistance to stripe rust in wheat line 03031-1-5 H62. Phytopathology. 108(1):103-113.

Interpretive Summary: Stripe rust is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. A mapping population of resistant wheat line 03031-1-5 H62 crossed with susceptible Avocet S was tested with race CYR32 of the stripe rust pathogen in fields. The resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K single nucleotide polymorphism (SNP) array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 kompetitive allele-specific PCR (KASP) markers were selected and used together with 84 simple sequence repeat (SSR) markers on 1B were used to genotype the mapping population. A 660K SNP array was used to identify more markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 had a large effect for stripe rust resistance, and mapped near the centromeric region of chromosome 1BS. Based on the origin, responses to different races of the stripe rust pathogen, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.

Technical Abstract: Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. In order to identify the resistance gene(s) in wheat line 03031-1-5 H62, which displayed high resistance to stripe rust at adult plant stage, a cross was made between 03031-1-5 H62 and susceptible cultivar Avocet S. The mapping population was tested with Chinese Pst race CYR32 through artificial inoculation in a field in Yangling, Shaanxi Province and in Tianshui, Gansu Province under natural infection. The segregation ratios indicated that the resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K SNP array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 KASP markers were selected and used together with 84 SSR markers on 1B were used to genotype the mapping population. To saturate the chromosomal region covering the YrH62 locus, a 660K SNP array was used to identify more SNP markers. To develop tightly linked markers for marker-assisted selection of YrH62 in wheat breeding, 18 SNPs were converted into KASP markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 explained 63.8% and 69.3 % of the phenotypic variation for disease severity and infection type, respectively. YrH62 was located near the centromeric region of chromosome 1BS based on the positions of the SSR markers in 1B deletion bins. Based on the origin, responses to Pst races, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes/QTL on 1B. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.