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作物学报 ›› 2024, Vol. 50 ›› Issue (5): 1115-1123.doi: 10.3724/SP.J.1006.2024.33052

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

用于玉米品种真实性鉴定的最优核心SNP位点集的研发

田红丽1**(), 杨扬1**(), 范亚明1**(), 易红梅1, 王蕊1, 金石桥2, 晋芳2, 张云龙1, 刘亚维1, 王凤格1,*(), 赵久然1,*()   

  1. 1北京市农林科学院玉米研究所 / 农业农村部农作物DNA指纹创新利用重点实验室(部省共建) / 玉米DNA指纹及分子育种北京市重点实验室, 北京 100097
    2全国农业技术推广服务中心, 北京 100125
  • 收稿日期:2023-10-25 接受日期:2024-01-12 出版日期:2024-05-12 网络出版日期:2024-02-08
  • 通讯作者: 赵久然, E-mail: maizezhao@126.com, Tel: 86-10-51503936; 王凤格, E-mail: gege0106@163.com, Tel: 86-10-51503558
  • 作者简介:田红丽, E-mail: tianhongli9963@163.com;
    杨杨, E-mail: caurwx@163.com;
    范亚明, E-mail: 13718078547@163.com第一联系人：

    **同等贡献

  • 基金资助:
    国家科技创新重大项目(2022ZD04019);北京市农林科学院财政项目(KJCX20230301);北京市农林科学院财政项目(CZZJ202206)

Development of an optimal core SNP loci set for maize variety genuineness identification

TIAN Hong-Li1**(), YANG Yang1**(), FAN Ya-Ming1**(), YI Hong-Mei1, WANG Rui1, JIN Shi-Qiao2, JIN Fang2, ZHANG Yun-Long1, LIU Ya-Wei1, WANG Feng-Ge1,*(), ZHAO Jiu-Ran1,*()   

  1. 1Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences / Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization of the Ministry of Agriculture and Rural Affairs (Co-construction by Ministry and Province) / Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097, China
    2National Agricultural Technology Extension and Service Center, Beijing 100026, China
  • Received:2023-10-25 Accepted:2024-01-12 Published:2024-05-12 Published online:2024-02-08
  • Contact: E-mail: maizezhao@126.com, Tel: 86-10-51503936; E-mail: gege0106@163.com, Tel: 86-10-51503558
  • About author:First author contact:

    **Contributed equally to this work

  • Supported by:
    National Scientific and Technological Innovation-Major Projects(2022ZD04019);Financial Project of Beijing Academy of Agriculture and Forestry Sciences(KJCX20230301);Financial Project of Beijing Academy of Agriculture and Forestry Sciences(CZZJ202206)

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摘要：

品种真实性是种子质量监测的一个重要指标。为建立准确可靠、快速简便、高通量、低成本的玉米品种真实性鉴定技术, 本文利用200个核心SNP位点构建的5816个玉米杂交品种, 3274个自交系的指纹数据, 基于遗传算法、品种识别率评估确定了一套高鉴别力的核心SNP位点集, 包含96个SNP位点。这96个SNPs全部位于基因内区域, 相对均匀分布在10对染色体上。采用上述杂交品种和自交系的指纹数据评估显示这96个位点具有较高多态性和品种区分能力, PIC、MAF、DP平均值分别为0.36、0.40、0.60和0.36、0.39、0.48, 对杂交品种、自交系的品种识别率达到99.14%和99.24%。两两样品成对比较结果显示, 99.99%的品种间差异位点数目≥3个, 杂交品种和自交系中96.74%和95.67%的成对比较差异位点数目集中在30~65个和30~60个。基于221个主推杂交品种的40个SSR位点、96个SNP位点的基因型数据分析结果显示, 这2组标记集的鉴定结果具有较高的一致性。综上所述, 本研究报道了一套具有位点数量最少、区分能力最强, 兼容多平台、适于自动化分型等优点的最优核心SNP集。期望位点集将在玉米品种真实性监测、种子质量控制中得到广泛应用, 进而维护玉米种子市场秩序、保障育种者权利以及保护农民利益。

关键词: 玉米品种, 真实性鉴定, SNP位点集, 高鉴别力

Abstract:

Variety genuineness is an important indicator for seed quality monitoring. In order to establish accurate, reliable, fast, simple, high-throughput, and low-cost maize variety genuineness identification technology, we evaluated and determined a set of high discriminative power core SNP loci set including 96 SNPs based on SNP fingerprint data of 5816 maize hybrids and 3274 inbred lines using the genetic algorithm and variety recognition rate. All 96 SNPs were located in the intra-gene region, generally distributed evenly on 10 pairs of chromosomes. The evaluation results using the above hybrid and inbred line data showed that 96 SNPs set had high polymorphism and variety discrimination power. The average values of PIC, MAF, and DP were 0.36, 0.40, 0.60, and 0.36, 0.39, 0.48 for hybrids and inbred lines, respectively. The variety discrimination power for hybrids and inbred lines reached 99.14% and 99.24%, respectively. Pairwise comparison between varieties showed that 99.99% of the comparisons had at least three differential loci. About 96.74% of hybrids and 95.67% of inbred lines mostly had the 30-65 and 30-60 differential loci between varieties, respectively. Compared with the 40 SSRs genotype dataset using 221 hybrids, the 96-SNPs set had high consistency in the identification results of the two marker sets. In summary, the optimal core SNPs set reported in this study had the advantage of the minimum number of loci, the highest discrimination power, the strongest differentiation platforms, and the automatic genotyping. It is expected that the extensive application of this core SNP loci set will be widely used in maize variety genuineness monitor and seed quality control for maintaining seed market order, so as to defend the breeders’ rights and protecting interests of farmers.

Key words: maize variety, genuineness identification, SNP loci set, high discrimination power

图1

最优位点集的品种识别率变化曲线图 横坐标为位点组合包含的位点数目, 纵坐标为品种识别率。"

图2

96个核心SNP位点在玉米核基因组上的分布"

图3

基于5816个杂交品种、3274个自交系评估96个SNP位点的PIC、MAF、DP和杂合基因型频率(AB rate)分布 横坐标为SNP位点, 排序依据PIC值由小到大的顺序; 纵坐标为各评估参数值。"

图4

玉米自交系和杂交品种分别成对比较差异SNP位点数目分布图"

图5

基于221个杂交品种两两遗传距离对96个SNP与40个SSR位点之间的相关性分析"

图6

20套三联体(杂交品种及其双亲)样品96个位点的SNP-DNA指纹展示图 每行代表1个样品, 每3行代表1套三联体样品, N01~N20为三联体样品的编号; 每列代表1个SNP位点, 按照在基因组上的物理位置排序; DNA指纹分别用不同颜色表示。"

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[2] 王兰珍;米国华;陈范骏;张福锁. 不同产量结构小麦品种对缺磷反应的分析[J]. 作物学报, 2003, 29(06): 867 -870 .
[3] 杨建昌;张亚洁;张建华;王志琴;朱庆森. 水分胁迫下水稻剑叶中多胺含量的变化及其与抗旱性的关系[J]. 作物学报, 2004, 30(11): 1069 -1075 .
[4] 袁美;杨光圣;傅廷栋;严红艳. 甘蓝型油菜生态型细胞质雄性不育两用系的研究Ⅲ. 8-8112AB的温度敏感性及其遗传[J]. 作物学报, 2003, 29(03): 330 -335 .
[5] 王永胜;王景;段静雅;王金发;刘良式. 水稻极度分蘖突变体的分离和遗传学初步研究[J]. 作物学报, 2002, 28(02): 235 -239 .
[6] 王丽燕;赵可夫. 玉米幼苗对盐胁迫的生理响应[J]. 作物学报, 2005, 31(02): 264 -268 .
[7] 田孟良;黄玉碧;谭功燮;刘永建;荣廷昭. 西南糯玉米地方品种waxy基因序列多态性分析[J]. 作物学报, 2008, 34(05): 729 -736 .
[8] 胡希远;李建平;宋喜芳. 空间统计分析在作物育种品系选择中的效果[J]. 作物学报, 2008, 34(03): 412 -417 .
[9] 王艳;邱立明;谢文娟;黄薇;叶锋;张富春;马纪. 昆虫抗冻蛋白基因转化烟草的抗寒性[J]. 作物学报, 2008, 34(03): 397 -402 .
[10] 郑希;吴建国;楼向阳;徐海明;石春海. 不同环境条件下稻米组氨酸和精氨酸的胚乳和母体植株QTL分析[J]. 作物学报, 2008, 34(03): 369 -375 .
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