利用全基因组关联研究鉴定影响面包小麦谷胱甘肽过氧化物酶活性的基因组区域。
Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study.
机构信息
Henan Institute of Crop Molecular Breeding, Postgraduate T & R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
Agronomy college, Zhengzhou University, Zhengzhou, 450001, China.
出版信息
BMC Plant Biol. 2021 Nov 10;21(1):523. doi: 10.1186/s12870-021-03299-6.
BACKGROUND
Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat.
RESULTS
Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59-12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000.
CONCLUSIONS
To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.
背景
过氧化物酶（POD）活性在面粉产品质量中起着重要作用，主要与面粉的褐变和漂白效果有关。在这里，我们使用由 207 个全球收集的小麦品种组成的关联群体对 POD 活性进行了全基因组关联研究（GWAS）。我们的研究还为小麦面粉颜色质量的遗传改良提供了基础。
结果
检测到与 POD 活性相关的 20 个数量性状位点（QTLs），解释了表型变异的 5.59-12.67%。优势等位基因与 POD 活性呈正相关。此外，成功开发了两个 SNP 用于 KASP（竞争性等位基因特异性 PCR）标记。两个 POD 基因 TraesCS2B02G615700 和 TraesCS2D02G583000 被排列在 QTL 侧翼基因组区域附近，但只有 TraesCS2D02G583000 在研究关联群体中高和低 POD 活性品种之间显示出显著的差异表达水平（P<0.001）。因此，它被推断为候选基因。TraesCS2D02G583000 的表达水平被指定为表达 GWAS（eGWAS）的表型，以筛选调控元件。总共在 20 条染色体（不包括 4D）上检测到 505 个显著 SNP，其中 9 个位于 TraesCS2D02G583000 内 1Mb 区间内。
结论
为了鉴定影响小麦籽粒 POD 活性的遗传位点，我们对 POD 活性和候选基因 TraesCS2D02G583000 表达进行了 GWAS。最终，检测到 20 个 POD 活性 QTL，而与两个 QTL 相关的 SNP 被转化为 KASP 标记，可用于标记辅助育种。通过 TraesCS2D02G583000 表达的 eGWAS 揭示了顺式和反式作用元件。本研究为在广泛遗传背景下提高 POD 活性提供了遗传位点，并大大提高了小麦的选择效率。
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