Genome-wide association analysis for yield and nitrogen efficiency related traits of wheat at maturity stage

Objectives To identify and locate stable molecular markers which are significantly correlated to the traits of yield and N efficiency of wheat under different N nutrition levels.

Methods A group of 134 wheat cultivars or lines were subjected to normal level N (required for 600 kg/hm² yield) and low level N (required for 400 kg/hm² yield) and four environmental treatments over two years. Fourteen traits related to yield and N efficiency of wheat were measured. Genome-wide association analysis using 90K SNP molecular markers was carried out for the tested traits by GLM + Q general linear model and MLM + K + Q mixed linear model.

Results The grain and straw yield under low N treatment were significantly lower than those under normal N treatment. The heritability of all the tested traits were above 75%. According to genome-wide association analysis on the 9329 SNPs, a total of 382 molecular marker sites located on 21 chromosomes were identified associating with 14 traits (P ≤ 0.001). Of all the identified marker sites, 305 (79.84%) were detected in only one environment; 77 sites were detected to be significantly associated with the same trait in at least two treatment environments; 9 SNP marker sites were detected in at least 3 environments and four environmental stable SNP marker sites were identified in at least four environments. The four stable markers (BobWhite_c47168 _598, Kukri_c31599_1456, wsnp_CAP11_c1761_958064 and Excalibur_c62826_254) were significantly related to number of grains per ear, grain N content, and number of spikelets. Twelve multi-trait co-location SNP marker sites which were simultaneously associated with at least three traits were located on chromosomes 2A, 3A, 4A, 5B, and 7B. Their average contribution rate ranged from 11.14% to 22.97%. The marker BobWhite_c47168_598 and Kukri_c31599_1456 were also located at two environmental stable sites (four environments). Candidate gene prediction was conducted in the region near stable sites (interval size estimated based on LD block and other methods) according to the SNP markers position of the 12 multi-trait co-location sites and four environmental stable sites. Gene function annotations of these genes were performed using the CDD tool of NCBI and Ensembl Plants website. According to the function annotations, a total of 10 candidate genes related to yield and nitrogen efficiency traits were determined.

Conclusions N accumulation was significantly and positively correlated with wheat yield. About 79.84% SNP marker sites which were significantly correlated with yield and N efficiency traits were detected only in specific environments. In addition, four environmental stable SNP markers were detected in four environments. Twelve molecular marker sites were significantly associated with three yield and nitrogen efficiency related traits simultaneously. This reflects the genetic hotspot which simultaneously control the yield and nitrogen efficiency traits. In summary, according to the environmental stable SNP marker sites and hotspots for different traits, we screened ten candidate genes related to yield and nitrogen efficiency. However, it will be worthy of further exploration.