Liu Jing, Xu Zhibin, Fan Xiaoli, Zhou Qiang, Cao Jun, Wang Fang, Ji Guangsi, Yang Li, Feng Bo, Wang Tao
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
Front Plant Sci. 2018 Oct 31;9:1584. doi: 10.3389/fpls.2018.01584. eCollection 2018.
Rapid detection of allelic variation and identification of advantage haplotypes responsible for spike related traits play a crucial role in wheat yield improvement. The released genome sequence of hexaploid wheat (Chinese Spring) provides an extraordinary opportunity for rapid detection of natural variation and promotes breeding application. Here, selection signals detection and genome-wide association study (GWAS) were conducted for spike related traits. Based on the genotyping results by 90K SNP chip, 192 common wheat samples from southwest China were analyzed. One hundred and forty-six selective windows and one hundred and eighty-four significant SNPs (51 for spike length, 28 for kernels per spike, 39 for spikelet number, 30 for thousand kernel weight, and 36 for spike number per plant) were detected. Furthermore, tightly linkage and environmental stability window clusters and SNP clusters were also obtained. As a result, four SNP clusters associated with spike length were detected on chromosome 2A, 2B, 2D, and 6A. Two SNP clusters correlated to kernels per spike were detected on 2A and 2B. One pleiotropy SNP cluster correlated to spikelet number and kernels per spike was detected on 7B. According to the genome sequence, these SNP clusters and their overlapped/flanking QTLs which have been reported previously were integrated to a physical map. The candidate genes responsible for spike length, kernels per spike and spikelet number were predicted. Based on the genotypes of cultivars in south China, two advantage haplotypes associated with spike length and one advantage haplotype associated with kernels per spike/spikelet number were detected which have not been effectively transited into cultivars. According to these haplotypes, KASP markers were developed and diagnosed across landraces and cultivars which were selected from south and north China. Consequently, KASP assay, consistent with the GWAS results, provides reliable haplotypes for MAS in wheat yield improvement.
快速检测等位基因变异并鉴定与穗部相关性状有关的优势单倍型在提高小麦产量中起着至关重要的作用。已公布的六倍体小麦（中国春）基因组序列为快速检测自然变异提供了绝佳机会，并推动了育种应用。在此，针对穗部相关性状进行了选择信号检测和全基因组关联研究（GWAS）。基于90K SNP芯片的基因分型结果，对来自中国西南地区的192份普通小麦样本进行了分析。检测到146个选择窗口和184个显著SNP（穗长相关51个、每穗粒数相关28个、小穗数相关39个、千粒重相关30个、单株穗数相关36个）。此外，还获得了紧密连锁且环境稳定性好的窗口簇和SNP簇。结果，在2A、2B、2D和6A染色体上检测到4个与穗长相关的SNP簇。在2A和2B上检测到2个与每穗粒数相关的SNP簇。在7B上检测到1个与小穗数和每穗粒数相关的多效性SNP簇。根据基因组序列，将这些SNP簇及其先前报道的重叠/侧翼QTL整合到一个物理图谱中。预测了与穗长、每穗粒数和小穗数相关的候选基因。基于中国南方品种的基因型，检测到2个与穗长相关的优势单倍型和1个与每穗粒数/小穗数相关的优势单倍型，这些单倍型尚未有效转化为品种。根据这些单倍型，开发了KASP标记，并在中国南方和北方选择的地方品种和栽培品种中进行了诊断。因此，与GWAS结果一致的KASP分析为小麦产量改良中的分子标记辅助选择提供了可靠的单倍型。
