• ISSN 1008-505X
  • CN 11-3996/S
张鹏霞, 周秀文, 梁雪, 郭营, 赵岩, 李斯深, 孔凡美. 小麦产量及氮效率相关性状的全基因组关联分析[J]. 植物营养与肥料学报, 2021, 27(6): 991-1003. DOI: 10.11674/zwyf.20549
引用本文: 张鹏霞, 周秀文, 梁雪, 郭营, 赵岩, 李斯深, 孔凡美. 小麦产量及氮效率相关性状的全基因组关联分析[J]. 植物营养与肥料学报, 2021, 27(6): 991-1003. DOI: 10.11674/zwyf.20549
ZHANG Peng-xia, ZHOU Xiu-wen, LIANG Xue, GUO Ying, ZHAO Yan, LI Si-shen, KONG Fan-mei. Genome-wide association analysis for yield and nitrogen efficiency related traits of wheat at maturity stage[J]. Journal of Plant Nutrition and Fertilizers, 2021, 27(6): 991-1003. DOI: 10.11674/zwyf.20549
Citation: ZHANG Peng-xia, ZHOU Xiu-wen, LIANG Xue, GUO Ying, ZHAO Yan, LI Si-shen, KONG Fan-mei. Genome-wide association analysis for yield and nitrogen efficiency related traits of wheat at maturity stage[J]. Journal of Plant Nutrition and Fertilizers, 2021, 27(6): 991-1003. DOI: 10.11674/zwyf.20549

小麦产量及氮效率相关性状的全基因组关联分析

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

  • 摘要:
    目的 探明控制产量及氮效率相关性状的稳定基因关联位点,为高产和氮素高效小麦育种及养分管理提供参考。
    方法 采用134个小麦品种 (系) 为试验材料,依据小麦产量水平600和400 kg/hm2的需氮量设置正常氮 (T1) 和低氮 (T2) 2个处理,进行了2年田间试验,共形成4个处理环境。对小麦成熟期与产量及氮效率相关的14个性状进行了表型鉴定,采用GLM + Q一般线性模型和MLM + K + Q混合线性模型相结合的方法,利用群体差异SNP分子标记 (90K SNP芯片) 对小麦产量和氮效率相关性状进行全基因组关联分析。
    结果 与正常氮处理相比,低氮处理条件下小麦籽粒产量、秸秆产量显著下降;所有性状的遗传力均在75%以上,其中小穗数的遗传力最高 (95.12%)。利用9329个SNP标记进行关联分析,共检测到382个SNP标记位点与供试14个性状存在显著关联(P ≤ 0.001),分布在21条染色体上。有305个 (79.84%) SNP标记位点仅在一个关联分析环境中被检测到;有77个位点在至少两种处理环境 (包含平均值环境) 中被检测到与同一性状显著关联 (稳定关联标记)。其中9个SNP标记位点在至少3个环境中被检测到。在4个环境下 (包括平均值环境) 均检测到的稳定关联位点有4个:BobWhite_c47168 _598、Kukri_c31599_1456、wsnp_CAP11_c1761_958064和Excalibur_c62826_254,分别与穗粒数、籽粒氮含量和小穗数显著关联;同时与至少3个性状显著关联的SNP标记位点共12个,分别位于2A、3A、4A、5B和7B染色体上,贡献率为11.14%~22.97%,其中,标记BobWhite_c47168_598和Kukri_c31599_1456还分别定位了两个多环境 (4种环境) 稳定位点。根据12个与多性状共同定位位点和4个多环境 (4个环境) 稳定位点关联的SNP标记位置获得稳定位点附近区域的基因 (基于LD block等方式估算的区间大小),使用NCBI中CDD工具和EnsemblPlants网站对这些基因进行基因功能注释,根据功能注释,共得到10个与产量和氮效率性状相关的候选基因。
    结论 氮供应水平对小麦成熟期产量和氮效率相关性状均有显著影响,氮素累积量与小麦产量显著正相关。本试验中检测到的与产量及氮效率相关性状显著关联的位点中,79.84%的SNP标记位点仅在一个氮处理环境中出现,环境稳定性较差;4个位点在4个环境条件下均被检测到,环境稳定性较好;12个SNP标记位点同时与至少3个性状显著关联,涉及性状均为产量及氮效率相关性状,反映了籽粒产量与氮素效率之间的显著相关关系,也可能是同时控制这些性状的遗传热点位点。根据这些热点位点和环境稳定性好的位点筛选到10个与产量及氮效率相关性状有关候选基因,值得深入探讨。

     

    Abstract:
    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.

     

/

返回文章
返回