Genetic Dissection Of New Wheat Varieties (Lines)in Henan Province

In order to explore the genetic basis of registered wheat varieties and new breeding lines in the past decades in Henan Province, the genetic structure, powdery mildew resistance and their resistance genes were evaluated and identified using high-throughput single nucleotide polymorphisms （SNP） assay and genome wide association mapping approaches. The main results obtained are as follows:1. The powdery mildew resistance of new wheat breeding varieties （lines） from2009-2013of Henan province was tested using Blumeria graminis f. sp. tritici （Bgt） isolates E09and E20. Molecular markers linked to powdery mildew resistance genes Pm2, Pm4a, Pm8, and Pm21were used to detect the presence of the individual resistance gene. Among908wheat varieties （lines） inoculated by E09,199（21.9%） of them exhibited resistance. Among412wheat varieties （lines） inoculated by E20,39（9.5%） of them exhibited resistance. Only15out of412（3.6%） varieties （lines） showed resistance to both E09and E20. The IRS chromatin was detected in580out of908（63.9%） wheat varieties （lines）, indicating the common use of Pm8or newly developed1BL/1RS translocation lines in wheat breeding program. Two varieties carried the board spectrum powdery mildew resistance gene Pm21originated from6AL/6VS translocation. Eight and two lines may contain the Pm2and Pm4a loci, respectively. More than one powdery mildew resistance genes were found in at least6lines.2. Thrity-six powdery mildew resistance wheat varieties were selected for large-scale powdery mildew resistance gene identification using the Illumina90K iSelect SNP chip and Bulked Segregate Analysis （BSA） approaches. SNP genotyping between36resistant bulks and36susceptible bulks revealed that single major polymorphic SNP peaks were identified on24of the36bulks. Among them, single polymorphic SNP peaks were found on chromosome2AL for20varieties （lines）, indicating a powdery mildew resistance gene, most likely on Pm4loci, was available in these varieties （lines）. However, known molecular markers Xgwm356and P1-P2linked to Pm4a and Pm4b were not effective to identify the powdery mildew resistance genes on2AL in the20varieties （lines） due to the genetic background divergence. A new marker wggc116-12for the powdery mildew resistance genes on2AL was developed and validated in two segregationg populations of Kai04131/Shi4185and Zhongyu9398/Shi4185, suggesting it could be used for marker assisted selection of the powdery mildew resistance gene on2AL in the20varieties （lines）. Single polymorphic SNP peaks were also detected between the resistant and susceptible bulks on chromosome2D,1B,6A and3B, respectively, for Zhengyumai518, Xinmai04077, Guomai301and Xiangyang3. The Pm21gene on6VS/6AL was further conformed in Guomai301by marker Xcau127. Multiple polymorphic SNP peaks were found between other12resistant and susceptible bulks, indicating more than one powdery mildew resistance genes may be available in these varieties （lines）.1BL/1RS translocations were detected in21varieties （lines）. However, only7of them showed single polymorphic SNP peaks on chromsome1B between the resistant and susceptible bulks, suggesting new1BL/1RS translocations different from Pm8derivatives were applied in the breeding program. Beside of this, single SNP peak was found between the resistant and susceptible bulks of Wanmai999, indicating a powdery mildew resistance gene is avaiable on chromosome1B in this none1BL/1RS translocation line. 3. Ninety-six registered wheat varieties in the past decade at Henan Province were seleted for SNP genotyping using the Illumina90k iSelect SNP chip. The results showed that47.39%of the SNPs （38661out of81587） were polymorphism between varieties. The genome distribution of polymorphic SNPs showed a tendency of B> A> D. The genetic similarity of the96varieties ranged from0.552to0.998with an average value of0.719. However, genetic similarity of0.652to0.812was found for94.3%of the tested varieties, indicating highly similarity for most of the varieties in Henan province. The96wheat varieties could be classified as seven groups by UPGMA analyses. Based on pedigree and SNP analyses, very narrow genetic background was observed for the registered varieties in the past decade in Henan province. It is an urgent task for wheat breeders to explore and introduce diversified germplasm resources into wheat breeding program to increase the yield potential and stress tolerance in the future.4. Genome wide association （GWAS） analyses were performed on10agronomic traits including heading date, mature period, maximum tillers, percentage of earbearing tiller, ears per mu, kernels per spike, thousand kernel weight, plant heigh, grain filling period, and grain filling rate, using the Illumina90k iSelect SNP genotyping and field trials data of94wheat varieties of Henan Province in3enviroments. A total of22,846polymorphic SNPs were used for TASSEL analysis with a general linear model and a mixed linear model. Using the general linear model, GWAS identified311SNP loci that explained10～30%of the phenotypic variations for individual traits, and42of them consistently reached genome-wide significance level. Seventy SNPs in chromosomes2A,2B,2D,3A,4D, and6A were found to be significantly associated with ears per mu （EPM）. SNP Excalibur_c2311₁839on3A explained the maximum （20.7%） phenotypic variation for ears per mu. For maximum tillers,121SNPs,86.78%of them located on chromosome3A, were identified and explained10.75～28.29%of the phenotypic variation. Thrity-one SNPs for percentage of earbearing tiller were detected on chromosomes1B,2A,7B and7D, and3of them consistently reached genome-wide significance level. Fourty-five SNPs explained14.63-30.28%of the phenotypic variations of plant heigh, and4of them consistently reached genome-wide significance level. Altegether,28SNPs on chromosomes2A,2D,3A,3B,3D,4A,5B,6B,7A,7B,7D were significantly associated with thousand kernel weight, and4of them consistently reached genome-wide significance level. Eight SNPs on chromosomes1A,2A,2D,4D, and7B were detected for mature period. Further more,7SNPs on chromosomes3A and5B were found for grain filling period, and2SNPs on chromosomes7B and7D were associated with grain filling rate. Moreover,3SNPs on chromosomes6D and7B were significantly associated with the heading date. Only one SNP Tdurum_contig67827₉8on chromosome2B was significantly associated with kernels per spike in genome-wide significance level. Meanwhile, pleiotropic effects were detected for several genomic regions responsible for different traits. There are47SNPs significantly associated with both ears per mu and maximum tillers,2SNPs significantly associated with both grain filling rate and thousand kernel weight,1SNPs significantly associated with plant heigh, mature period and maximum tillers, and1SNPs significantly associated with the maximum tillers and percentage of earbearing tiller. Using the mixed linear model, only3SNPs were identified by GWAS for percentage of earbearing tiller.