Genome-Wide Association Analysis Of Plant Height Traits And Spike Related Traits In Wheat

Wheat（Triticum aestivum L.）is one of the major staple food crops worldwide.Due to the fast increase of the world’s population and climate change,the demand for wheat is increasing.Therefore,selection and breeding elite wheat varieties having stable-yield and high grain quality are one of the major targets for sustainability in wheat supply.Wheat is one of the three major grain crops in China.Winter wheat is majorly grown in the middle and lower reaches of the Yangtze River,where is one of the major wheat-producing areas in southern China and the farming system mainly follows rice-wheat rotations.However,in recent years,due to the expansion of the direct-seeding rice area in the middle and lower reaches of the Yangtze River（for a purpose to ensure a stable rice yield）,the requirement of early maturity and late sowing capable wheat varieties is only increasing.Late sowing in wheat significantly shortens the growth period,and reduces the number of spike per plant,grains per spike and thousand-grain weight,ultimately leading to the yield penalty in current wheat cultivars.To conquer this issue,breeding elite wheat varieties suitable for late sowing but with early maturity will well suit modern agricultural system and address this problem.Based on the literature study on domestic wheat production traits,plant height traits,inheritance trait and gene mapping,plus the influence of cultivation conditions on the two related traits,a natural population consisting of 327 wheat varieties（lines）was used in this research to select latesowing suitable and early-maturing wheat varieties.Wheat plant height traits and spike related traits from 2 locations × 3 sowing dates × 3 replications after maturity were investigated to identify the differences in stable performance of each trait,supplying clues for screening and providing elite germplasm resources utilized for breeding late-sowing suitable and earlymaturing wheat varieties.We analyzed the genotypes and population structure of the natural population through GBS sequencing.Genome-wide association analysis was carried out for each phenotyping trait from normal sowing and late sowing trials to screen molecular markers stably associated with wheat plant height and spike related traits.Allele types and effects of stable association loci were analyzed with candidate genes prediction for individual stable loci.The main results are as bellows:1.Mean value of all traits in Yangzhou consistently decreased along with the delay of the sowing dates.In Yancheng,except for the average plant height and spike length which gradually decreased along with the delay of the sowing period,the mean values of the other three traits were the highest in the second sowing period.Under multiple environments,the generalized heritability was represented as plant height（98.45%）,internode length below spike（97.08%）,spike length（95.04%）,spikelet number per spike（91.34%）and the number of spike per plant（87.61%）,respectively.While there is no significant difference in plant height,internode length below spike among varieties and sowing dates,and no difference in spikelet number per spike among locations,other traits all indicated significant or extremely significant differences,among varieties,locations,sowing dates,variety and location interactions,variety and sowing date interactions.Ten wheat varieties including Xiangmai 35,Pingyang 27,Huaimai 23,Huaimai 22,Emai 6,Zhenmai 12,Xiaoyan 81,Shannong 7859,Annong 1589,and Shuiyuan 86 indicated stable performance and high capability of late sowing,which could be selected as parent lines in breeding early-maturing wheat varieties suitable for late sowing.2.A total of 601Gb clean data was obtained by sequencing this natural population through GBS technology,bringing the average size of 1.8Gb data from each sample.Overall Q30 was 89.10%and GC content was 39.24%.264924 high-quality SNPs were obtained after quality control,of which the number of SNP markers on chromosome 4D was the least（1315）,whilst the number of SNP markers on chromosome 3B was the largest（27617）.The density of SNP markers on chromosome 1A was the highest,and that on chromosome 4D was the lowest.This natural population can be divided into 3 subgroups,including 96 wheat varieties（lines）mostly from landraces;133 wheat varieties（lines）mainly from the Huanghuai area,as such of Henan and Shandong;98 wheat cultivars（lines）mostly from the middle and lower Yangtze regions.The genetic relationship analysis on this population indicated non-genetic relationships among most varieties（lines）,adding feasibility of utilizing this population for genome-wide association analysis in this study.3.Under normal sowing dates,7 SNPs significantly correlated with wheat plant height in Yangzhou were identified on chromosomes 1B,2A,4B,4D,5A,5B and 7D,contributing to a phenotypic variation（PVE）range of 1.77%to 46.90%;Meanwhile,5 SNPs significantly correlated with wheat internode length below spike were identified on chromosomes 3 A,4A,4B,4D and 7A,producing a PVE ranged of 1.29%to 62.68%;Wheat spike length was significantly correlated with a SNP located at 24057574bp on chromosome 2D with a PVE of 66.11%;8 SNPs were significantly correlated with spikelet number per spike and identified on 2A,2B,2D,3B,4A,6A and 7D,with a PVE ranged from 5.96%-31.49%;There were 5 SNPs that were significantly correlated with the number of spike on chromosomes 1B,3B,4B,7A,and 7B,and the PVE ranged from 0.98%-40.57%.In Yancheng,6 SNPs were significantly associated with wheat plant height,located on chromosomes 2A,4B,4D,5A,6A,and 7D,respectively,with a PVE ranging from 2.04%to 39.03%;5 SNPs were significantly correlated with wheat internode length below spike and located on chromosomes 1A,4B,4D,5A,and 7D with a PVE of 5.06%-57.91%;There were 4 SNPs on chromosomes 2D,5A,and 6B that were significantly correlated with wheat spike length.The PVE ranged from 12.61%to 37.53%.A total of 5 SNPs significantly related to spikelet number per spike have been found on chromosomes 2A,2D,4B,5A,and 6A.Their PVE ranged from 2.71%to 31.34%;There were 7 SNPs significantly correlated with number of spike.They were located on chromosomes 2A,2B,3 A,3B,5A,5B,and 6A,and the PVE ranged 0.14%～31.19%.4.With different sowing dates,3 stable loci were consistently detected regarding plant height,which were located on chromosomes 4B,4D,and 5A,respectively.Among which 4B₃3302589 and 4D₂2474131 were completely consistent in two locations and six different sowing dates.Based on the genotype of the associated markers in natural population,it was found that the average plant height of varieties carrying alt-type allelic variation was significantly lower than the average plant height of varieties carrying ref-type allelic variation,among which 4B₃3302589 can reduce the plant height by 22.14%-26.66%,4D₂2474131 can reduce the plant height by 24.80%-29.78%,and 5A₅36164590 can reduce the plant height by 30.00%-37.31%in different locations.The average plant height of lines carrying three alt-type variations was lower than those with two alt-type variations.Combined with the reference genome annotations,three candidate genes for plant height were obtained in the LD block containing SNP 5A₅36164590,namely TraesCS5A03G0785300,TraesCS5A03G0785400,and TraesCS5A03G0785500.A few loci associated with spike related traits were detectable under multiple locations.A significant correlation was found between spikelet number per spikelet and markers 2D 66461351,2D₆7697689,2D₆8412934,and 2D₇2890387,which were all located within the same interval of LD decay distance;Markers with consistent positions（1A₃51716140 and 1A₃48948242）were significantly correlated with the number of spike under the first sowing date and the third sowing date.It was found that the average spikelet number per spikelet and number of spike of varieties carrying alt-type allelic variation were significantly higher than those carrying reftype allelic variation,among which 2D 68412934 and 1A₃48948242 can increase the spikelet number per spikelet and number of spike by 1.41%-5.27%and 14.59%-53.90%in different locations,respectively.The results of this study add foundations of discovering stable and novel loci and developing molecular markers for modifying wheat plant height and spike related traits.