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作物学报

作物学报 ›› 2026, Vol. 52 ›› Issue (5): 1341-1352.doi: 10.3724/SP.J.1006.2026.53070

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于RNA-Seq和BSA-Seq联合分析挖掘玉米侧根密度基因资源

韩亚鑫1,2(), 何冠华2,*(), 张小琼1,2, 张登峰2, 李永祥2, 刘旭洋2, 王天宇2, 黎裕2, 邹华文1,*(), 李春辉2,*()   

  1. 1 长江大学农学院, 湖北荆州 434025
    2 作物基因资源与育种全国重点实验室 / 中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2025-09-12 接受日期:2026-01-22 出版日期:2026-05-12 网络出版日期:2026-02-11
  • 通讯作者: *何冠华, E-mail: heguanhua@caas.cn; 邹华文, E-mail: zouhuawen@yangtzeu.edu.cn; 李春辉, E-mail:lichunhui@caas.cn
  • 作者简介:E-mail: 1412147019@qq.com
  • 基金资助:
    国家自然科学基金项目(32201751);财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-0204);中国农业科学院创新工程项目资助。

Identification of maize lateral root density genes resources through integrated RNA-seq and BSA-seq analyses

Han Ya-Xin1,2(), He Guan-Hua2,*(), Zhang Xiao-Qiong1,2, Zhang Deng-Feng2, Li Yong-Xiang2, Liu Xu-Yang2, Wang Tian-Yu2, Li Yu2, Zou Hua-Wen1,*(), Li Chun-Hui2,*()   

  1. 1 College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    2 State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2025-09-12 Accepted:2026-01-22 Published:2026-05-12 Published online:2026-02-11
  • Contact: *He Guan-Hua, E-mail: heguanhua@caas.cn; Zou Hua-Wen, E-mail: zouhuawen@yangtzeu.edu.cn; Li Chun-Hui, E-mail:lichunhui@caas.cn
  • Supported by:
    National Natural Science Foundation of China(32201751);China Agriculture Research System of MOF and MARA(CARS-0204);Innovation Program of Chinese Academy of Agricultural Sciences.

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摘要：

根系作为玉米植株吸收水分和营养成分的重要器官, 对玉米生长发育及产量形成至关重要。因此研究玉米根系结构的遗传机制对玉米高产育种实践具有重要意义。本研究利用玉米自交系丹黄02 (侧根密度高)和HRB16041 (侧根密度低)构建了一个F2群体, 利用极端性状混池测序法(BSA-seq)获得控制侧根密度(LRD)的显著关联位点, 结合8个玉米自交系侧根组织的转录组测序, 挖掘控制玉米苗期侧根密度的候选基因。基于侧根密度的BSA-seq分析, 研究共检测到240个显著关联的SNP和2420个显著关联的InDel位点, 其中, 位于基因上下游区域或影响可变剪接位点和基因编码蛋白的变异位点共涉及235个候选基因。通过侧根组织RNA-seq分析, 共鉴定出与侧根密度相关的差异表达基因1979个, 其中, 954个基因上调表达, 1025个基因下调表达。BSA-seq和RNA-seq分析共同鉴定到了12个基因, 这些基因被确定为控制侧根密度的候选基因。通过对这12个候选基因进行qRT-PCR验证, 确定Zm00001d033708和Zm00001d045720等候选基因的基因表达和玉米侧根密度呈正相关, 而Zm00001d040375基因表达与玉米侧根密度呈负相关。本研究为玉米侧根密度研究提供了候选基因资源。

关键词: 玉米, 侧根密度, 混池测序, 转录组分析, 表达量

Abstract:

As the primary organ responsible for water and nutrient uptake, the root system plays a vital role in maize growth and yield formation. Understanding the genetic basis of root architectural traits—particularly lateral root density (LRD)—is crucial for advancing high-yield breeding strategies. In this study, an F2 population was developed from a cross between Danhuang 02 (high LRD) and HRB16041 (low LRD). Bulked segregant analysis coupled with high-throughput sequencing (BSA-seq) was conducted to identify genomic loci significantly associated with LRD. In parallel, transcriptome sequencing of lateral root tissues from eight diverse maize inbred lines was performed to explore candidate genes regulating LRD at the seedling stage. BSA-seq identified 240 significantly associated SNPs and 2420 InDels, involving 235 candidate genes located in regulatory regions, alternative splicing sites, or coding sequences. RNA-seq analysis revealed 1979 differentially expressed genes (DEGs) associated with LRD, including 954 up-regulated and 1025 down-regulated genes. Integrated analysis of BSA-seq and RNA-seq data identified 12 overlapping genes as strong candidates for regulating LRD. qRT-PCR validation suggested that Zm00001d033708 and Zm00001d045720 may act as positive regulators of lateral root density, while Zm00001d040375 may function as a negative regulator. This study provides valuable genetic resources and candidate genes for understanding and improving lateral root development in maize.

Key words: maize, lateral root density, bulked segregant analysis, transcriptome analysis, expression level

表1

本研究所使用的引物"

引物名称
Primer name		 引物序列
Primer sequence (5′-3′)
Zm00001d033708-F AATTCCCTGCATCCAGACCG
Zm00001d033708-R GGAACAACCCATTCTGGGCA
Zm00001d034546-F CCTCCATGACGATGCTACACT
Zm00001d034546-R GAAACGAAAACCTCCACAGGC
Zm00001d040315-F AGGAAGAAGCTCGATGACGC
Zm00001d040315-R TGGACCACCACCGCTATTTC
Zm00001d040375-F TGGTAAAGTTGCCACCGTAG
Zm00001d040375-R TTGCAGTTCGCGGCAGTTA
Zm00001d042901-F CCGACCTCCCAAAATGCTGA
Zm00001d042901-R GCAGGAAGCAGGAGAACCTT
Zm00001d045720-F GCGATACAAGCGGAGGAGTT
Zm00001d045720-R GGCTGCCACAGACGATACTT

图1

亲本表型及混池构建方法 A: 丹黄02和HRB16041的侧根密度表型; B: F2群体的侧根密度表型正态分布图。LRD: 侧根密度。"

图2

SNP-index和InDel-index在染色体上的分布"

表2

基于BSA分析的候选基因及其功能注释"

染色体
Chr.		 基因
Gene		 变异a
Variant a		 基因功能注释
Gene functional annotation
1 Zm00001d028400 U, FI(2) Pathogenesis-related thaumatin superfamily protein
3 Zm00001d039542 FI Phospholipase A1-igamma1 chloroplastic
3 Zm00001d040252 FI Heavy metal-associated isoprenylated plant protein 39
3 Zm00001d041745 FD Unknown
3 Zm00001d042347 FD Transcription elongation factor 1 homolog
3 Zm00001d042393 FD Protein arginine methyltransferase NDUFAF7
3 Zm00001d042753 N Transcription repressor OFP13
3 Zm00001d042964 U (3), FD (2) Unknown
3 Zm00001d043126 FD Ulp1 protease family C-terminal catalytic domain containing protein expressed
3 Zm00001d043420 FD Basic leucine zipper 34
5 Zm00001d013405 S Protein kinase superfamily protein
5 Zm00001d013819 FI Galactose mutarotase-like superfamily protein
9 Zm00001d045721 FD TRICHOME BIREFRINGENCE-LIKE 20
9 Zm00001d047495 FD Premnaspirodiene oxygenase
10 Zm00001d024359 FD Alpha-humulene/(-)-(E)-beta-caryophyllene synthase
10 Zm00001d025255 FD Putative DUF26-domain protein kinase
10 Zm00001d025522 FD (2) Putative FKBP-type peptidyl-prolyl cis-trans isomerase family protein
10 Zm00001d025821 N Putative DUF231 domain containing family protein
10 Zm00001d025952 FI NAD(P)H-quinone oxidoreductase subunit M chloroplastic
10 Zm00001d026021 FD (2), FI (2) Putative RING zinc finger domain superfamily protein
10 Zm00001d026120 FI Putative HLH DNA-binding domain superfamily protein

图3

8个玉米自交系侧根密度及转录组基因表达分析图 A: 8个玉米自交系的侧根密度表型变化; B: 转录组差异表达基因中的编码蛋白基因聚类分析; C: 转录组差异表达基因中的非编码蛋白基因聚类分析。Zheng 58: 郑58。"

图4

差异表达基因分析 A: 基因表达韦恩图; B: 簇4差异表达基因火山图; C: 差异表达基因的GO富集分析; D: 差异表达基因的KEGG富集分析。MLR: 侧根密度大; FLR: 侧根密度小。"

图5

BSA-seq和RNA-seq候选基因的韦恩图"

表3

候选基因信息及功能注释"

基因
Gene		 基因功能注释
Gene functional annotation		 RNA-seq a BSA-seq b
Zm00001d033708 mRNA cap guanine-N7 methyltransferase Up Downstream
Zm00001d034546 Cupredoxin superfamily protein Up Upstream
Zm00001d039567 LRR protein WM1.10 Up Upstream
Zm00001d040298 FPF1-like protein 1 Up Upstream
Zm00001d040315 Unknown Up Upstream (2)
Zm00001d040375 Triosephosphate isomerase cytosolic Down Downstream
Zm00001d042901 L-ascorbate oxidase Up Upstream
Zm00001d043149 Leucine-rich repeat (LRR) family protein Up Upstream
Zm00001d045139 Vacuolar proton pump homolog 1 Up Upstream
Zm00001d045720 TRICHOME BIREFRINGENCE-LIKE 20 Up Upstream
Zm00001d025229 Unknown Down Upstream
Zm00001d025325 Desiccation-related protein PCC13-62 Up Upstream

图6

侧根密度候选基因的qRT-PCR分析 **表示在0.01水平差异显著, ***表示在0.001水平差异显著, ****表示在0.0001水平差异显著。Zheng 58: 郑58, 侧根密度小的自交系; PHN46: 侧根密度大的自交系; HRB16041: 侧根密度小的自交系; Danhuang 02: 丹黄02, 侧根密度大的自交系。"

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