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作物学报

作物学报 ›› 2026, Vol. 52 ›› Issue (3): 780-789.doi: 10.3724/SP.J.1006.2026.53051

所属专题： 玉米：遗传育种·种质资源·分子遗传学

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于BSA-seq技术定位玉米籽粒花青素关联基因

张超1,2,*(), 郭欢1, 李忠玲1, 岳淑宁1, 赵娜1   

  1. 1陕西植物线虫重点实验室 / 陕西省生物农业研究所, 陕西西安 710043
    2青海省农林科学院 / 青海大学, 青海西宁 810016
  • 收稿日期:2025-07-16 接受日期:2025-11-18 出版日期:2026-03-12 网络出版日期:2025-12-10
  • 通讯作者: *张超: E-mail: zhangc@xab.ac.cn
  • 基金资助:
    陕西省科技厅青年基金项目(2024JC-YBQN-0194);陕西省科学院种子基金项目(2022K-18);西安市科技局农业技术攻关一般项目(2024JH-NYYBN0175);陕西省生物农业研究所青年项目(2023SY01);陕西省科学院基础研究面上项目(2023K-13);陕西省科学院应用技术研发项目(2025K-05)

Mapping genes associated with anthocyanin in maize kernels using BSA-seq technology

Zhang Chao1,2,*(), Guo Huan1, Li Zhong-Ling1, Yue Shu-Ning1, Zhao Na1   

  1. 1Shaanxi Key Laboratory of Plant Nematology / Bio-Agriculture Institute of Shaanxi, Xi’an 710043, Shaanxi, China
    2Qinghai Academy of Agricultural and Forestry Sciences / Qinghai University, Xining 810016, Qinghai, China
  • Received:2025-07-16 Accepted:2025-11-18 Published:2026-03-12 Published online:2025-12-10
  • Contact: *张超: E-mail: zhangc@xab.ac.cn
  • Supported by:
    Shaanxi Provincial Natural Science Foundation Youth Project(2024JC-YBQN-0194);Seed Fund of Shaanxi Academy of Sciences(2022K-18);General Project of Agricultural Technology Research of the Xi’an Municipal Science and Technology Bureau(2024JH-NYYBN0175);Youth Basic Research Project of Bio-Agriculture Institute of Shaanxi(2023SY01);General Program for Basic Research Project of Academy of Sciences(2023K-13);Applied Technology Research and Development Project of Shaanxi Academy of Sciences(2025K-05)

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摘要：

花青素作为鲜食玉米的表型之一, 使其具有更高的营养价值和经济价值。为了研究玉米籽粒中花青素的关联基因, 本研究利用连续自交多代的黑糯和白糯玉米作为亲本材料构建获得F2代分离群体。于F2:3统计玉米籽粒颜色表明, 黑白粒占比表现为极显著差异。利用BSA-seq技术对黑粒和白粒的表型混池样本进行基因组测序, 挖掘花青素积累的关联基因。通过表型和基因测序联合分析, 玉米籽粒中花青素合成的关联基因片段主要位于6号染色体的107.9 ~113.2 Mb区域内。候选区域内共注释到116个基因, 其中包括53个非同义突变基因, 17个移码突变基因。通过基因注释信息分析, 推测出花青素结构基因Zm00001eb276450 (ANR)、转录因子基因Zm00001eb276870 (WD40)和Zm00001eb276640 (MYB)可能为玉米籽粒中花青素关联的候选基因。该研究结果为进一步完善玉米籽粒花青素关联基因的功能解析奠定了重要基础, 也为快速筛选花青素鲜食玉米新品种提供了参考基因。

关键词: 鲜食玉米, 花青素, BSA-seq, 表型-基因型关联分析, 序列差异

Abstract:

Anthocyanin is a phenotypic trait in fresh corn that enhances both its nutritional and economic value. To identify genes regulating anthocyanin accumulation in maize kernels, we developed an F2 segregating population by crossing black and white waxy maize lines, followed by self-pollination. Statistical analysis of kernel coloration in the F2:3 population revealed a highly significant segregation between black and white phenotypes, prompting bulked segregant analysis sequencing (BSA-seq) of phenotype-based pools. Integrating phenotypic data with genome sequencing, we mapped the anthocyanin-associated locus to a 107.9-113.2 Mb region on chromosome 6. Within this interval, 116 annotated genes were identified, including 53 genes with nonsynonymous mutations and 17 with frameshift mutations. Gene annotation highlighted three key candidates potentially involved in anthocyanin biosynthesis: Zm00001eb276450 (ANR), Zm00001eb276870 (WD40), and Zm00001eb276640 (MYB). These findings provide a valuable foundation for elucidating the genetic mechanisms underlying anthocyanin accumulation in maize kernels and offer promising candidate genes for the rapid development of fresh-eating maize varieties with enhanced anthocyanin content.

Key words: fresh corn, anthocyanin, BSA-seq, phenotype-genotype association analysis, sequence differences

表1

候选基因定量引物设计"

基因名称
Gene name		 引物序列
Primer sequence (5′-3′)
ACTIN F: CCAAGGCCAACAGAGAGAAA
R: TCACCGGAATCCATCACAATAC
Zm00001eb276450 F: CCTGCCGCTGGTTCACAT
R: GGCGATGGTCGTGTTGAG
Zm00001eb276870 F: GGTGACTGGATTGGGACT
R: AGACGCCTAAGCGACCAC
Zm00001eb276640 F: CTGGACCAACCACCTTAG
R: GTTTCAGAACAACCCTCA
Zm00001eb276630 F: CCCAACTGCCTTCAAAGT
R: GACGCTATCGGTCTCCTC
Zm00001eb276620 F: GTATTTGAGCACCTTGACT
R: CAATGGCACTACCAACAG

附图1

黑粒、白粒和红粒的表型差异"

附表1

籽粒颜色遗传模型分析"

遗传模型
Genetic model		 名称
Name		 实测值
Observed value (O)		 理论值
Expected value (E)		 O-E (O-E)2 (O-E)2 / E χ2
相加型变式(9∶6∶1)
Additive Model (9∶6∶1)		 黑粒Black kernels 342 334.125 7.875 62.016 0.186 10.606
红粒Red kernels 198 222.750 -24.750 612.563 2.750
白粒White kernels 54 37.125 16.875 284.766 7.670
总计Total 594 594.000 — — —
显性上位变式(12∶3∶1)
Dominant epistatic model (12∶3∶1)		 黑粒Black kernels 342 445.500 -103.500 10,712.250 24.045 99.091
红粒Red kernels 198 111.375 86.625 7503.891 67.375
白粒White kernels 54 37.125 16.875 284.766 7.670
总计Total 594 594.000 — — —
重叠作用变式(15∶1)
Duplicate gene model (15∶1)		 有色Colored 540 556.875 -16.875 284.766 0.511 0.511
无色Colorless 54 37.125 16.875 284.766 7.670
总计Total 594 594.000 — — —

图1

黑籽粒和白籽粒群体花青素类物质含量检测分析 A: 黑、白粒玉米籽粒照片; B: 黑、白粒玉米籽粒花青素类物质含量。"

表2

测序样本DNA测序质量分析"

样本
Sample		 过滤读取数
Clean reads		 过滤碱基数
Clean base		 Q30 (%) 靶定参考基因组
Properly mapped (%)		 覆盖深度
Coverage depth		 10 ×覆盖深度比例
Cov_ratio_10 × (%)
黑粒Black kernels 535,674,944 79,865,813,648 95.73 82.81 35 85.41
白粒White kernels 517,409,140 76,429,320,409 96.02 78.68 34 84.22

表3

样本间SNP和InDel类型和数量分析"

样本
Sample		 SNP数量
SNP number		 转换型SNP数量
Number of transition SNPs		 颠换型SNP数量
Number of transversion SNPs		 杂合类型比率
Heterozygous genotype ratio		 CDS插入变异
Number of CDS-insertion		 CDS缺失变异
Number of CDS-deletion
黑粒Black kernels 10,355,335 7,446,721 2,908,614 0.7731 14,864 15,989
白粒White kernels 9,551,131 6,860,013 2,691,118 0.6663 13,832 14,885
总计Total 12,590,579 9,065,232 3,525,347 — 17,593 18,443

图2

黑粒和白粒基因混池分析 A: SNP位点与表型关联分析: 左图为ED关联值在染色体上的分布, 右图为SNP-Index关联值在染色体上的分布; B: InDel位点与表型关联分析: 左图为ED关联值在染色体上的分布, 右图为InDel-Index关联值在染色体上的分布(上图是隐性混池的InDel-Index值的分布图, 中图是显性混池的InDel-Index值的分布图, 下图是ΔInDel-Index值的分布图, 其中红色的线代表置信度为0.99的阈值线, 蓝色的线代表置信度为0.95的阈值线, 绿色的线代表置信度为0.90的阈值线)。"

图3

4种计算方法连锁关联共有基因韦恩图 SNP: 单核苷酸多态性; InDel: 插入缺失标记; ED: 欧式距离算法。"

图4

候选基因qRT-PCR分析 ***表示在0.001水平上差异显著; ns表示差异不显著。"

图5

黑粒、白粒玉米植株中Zm00001eb276450 (ANR)基因序列比对"

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