花生全基因组变异的鉴定和InDel标记的开发及应用
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1.广东省省级现代农业耕地保育与节水农业产业技术研发中心;2.湛江市农业科学院

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海南省自然科学基金


Genome-wide Variation Identification in peanut and Development of InDel Markers for Genetic Research
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1.Guangdong Modern Agriculture Cultivated Land Conservation and Water-saving Agriculture Industrial Technology Research and Development Center,Zhanjiang Experiment Station,Chinese Academy of Tropical Agricultural Science,Zhanjiang;2.Zhanjiang Academy of Agricultural Sciences,Zhanjiang

Fund Project:

Hainan Provincial Natural Science Foundation of China

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    摘要:

    鉴定花生全基因组变异,明确全基因组InDel的分布特点,开发并验证InDel标记,评估InDel标记在花生亲缘关系和品种鉴定中的效率。本研究利用13 个花生品种的重测序数据进行了全基因组变异鉴定,共检测313432 个高质量SNP和38777 个高质量InDel,平均分布密度分别为123 个/Mb和15.23 个/Mb。InDel和SNP主要分布于基因间区域,分别占52.35%和60.08%,其次是上游基因和下游基因序列内,共占36.12%和32.49%。利用插入或缺失长度≥10 bp的位点进行设计,3675 个InDel位点可以进行引物设计,这些位点在花生20 条染色体上不均匀分布,标记密度范围为1.08(Chr02)~2.45(Chr08),平均1.48 个/Mb;e-PCR检测表明2561 对引物(69.69%)扩增位点为1~3 个,根据引物扩增位点在栽培种花生基因组中的位置信息绘制了扩增位点的物理图谱。在100 对随机引物中,共有31 对在4 个亲缘关系较远的花生品种中存在差异条带;31 对InDel引物在47 份花生品种(或育种系)中共检测到62 个等位变异,主基因频率范围为0.51~0.98,平均为0.77;PIC信息量范围为0.04~0.37,平均为0.24。聚类分析和群体结构分析均可将47 份花生品种(或育种系)分为2 个类群,且结果基本一致;47 份材料最少可用7 个标记进行区分,表明开发的InDel标记可以有效的用于花生遗传多样性的评估和品种鉴定。研究结果丰富了花生的分子标记,为InDel标记在花生资源遗传多样性、品种鉴定、指纹图谱构建等遗传研究中的利用提供了理论基础。

    Abstract:

    This study aimed to identify genetic variation in peanut genome,clarify their distribution characteristic,develop and verify InDel markers, and evaluate the efficiency of InDel markers in peanut cultivar identification. Genome resequencing data of 13 peanut cultivars were used to identify genome-wide variations, and a total of 313,432 high-quality SNPS and 38,777 high-quality InDel were detected, with an average distribution density of 123 and 15.23 /Mb, respectively. The InDels and SNPs were mainly distributed in intergenic regions, with a frequency of 52.35% and 60.08%, respectively, followed by upstream and downstream gene sequences, accounting for 36.12% and 32.49%. Primers were designed using InDel with insertion or deletion length ≥10 bp, and 3,675 InDel could be used to develop InDel markers. These InDel locus were unevenly distributed on the 20 chromosomes of peanut, and the marker density ranged from 1.08 (Chr02) to 2.45 (Chr08), with an average of 1.48 /Mb. Using electronic PCR, 2561 pairs of primers (69.69%) amplified 1~3 effective loci in the peanut reference genome. The physical map of amplification loci was drawn according to the loci position in cultivated peanut genome. Among 100 pairs of random primers, 31 pairs amplified different bands in the 4 varieties with distant relatives. The 31 InDel primer pairs amplified 62 alleles in 47 peanut varieties (or breeding lines), the frequency of major genes ranged from 0.51 to 0.98 with an average of 0.77, and the PIC information ranged from 0.04 to 0.37, with an average of 0.24. Both cluster analysis and population structure analysis could divide the 47 peanut varieties (or breeding lines) into two groups, and the 47 materials could be distinguished by at least 7 markers, indicating that the developed InDel markers could be effectively used for the assessment of genetic diversity and variety identification of peanut. The research results enriched the molecular markers of peanut, and provided a theoretical basis for the use of InDel markers in genetic studies of peanut resource genetic diversity, variety identification, fingerprint construction.

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  • 收稿日期:2024-02-06
  • 最后修改日期:2024-05-09
  • 录用日期:2024-09-02
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