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作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (4): 969-981.doi: 10.3724/SP.J.1006.2025.44158

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

花生荚果产量相关性状QTL定位与候选基因分析

林伟津1,2(), 郭泽佳1,2, 刘浩1, 李海芬1, 王润风1, 黄璐1, 余倩霞1, 陈小平1, 洪彦彬1, 李少雄1,*(), 鲁清1,*()   

  1. 1广东省农业科学院作物研究所 / 广东省农作物遗传改良重点实验室 / 国家油料作物改良中心南方花生分中心, 广东广州 510640
    2华南农业大学农学院, 广东广州 510642
  • 收稿日期:2024-09-19 接受日期:2024-12-12 出版日期:2025-04-12 网络出版日期:2024-12-19
  • 通讯作者: 李少雄, E-mail: lishaoxiong@gdaas.cn; 鲁清, E-mail: luqing@gdaas.cn
  • 作者简介:E-mail: 649087805@qq.com
  • 基金资助:
    国家自然科学基金项目(32172051);国家自然科学基金项目(32301869);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-13);国家重点研发计划项目(2023YFD1202800);省级乡村振兴战略专项资金种业振兴项目(2024);广东省重点领域研发计划项目-现代种业(2022B0202060004);广东省基础与应用基础研究基金面上项目(2023A1515010098);广东省基础与应用基础研究基金面上项目(2024A1515010511)

QTL mapping and candidate gene analysis of peanut pod yield-related traits

LIN Wei-Jin1,2(), GUO Ze-Jia1,2, LIU Hao1, LI Hai-Fen1, WANG Run-Feng1, HUANG Lu1, YU Qian-Xia1, CHEN Xiao-Ping1, HONG Yan-Bin1, LI Shao-Xiong1,*(), LU Qing1,*()   

  1. 1Crop Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of Crop Genetic Improvement / National Oilseed Crop Improvement Center Southern Peanut Subcenter, Guangzhou 510640, Guangdong, China
    2College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
  • Received:2024-09-19 Accepted:2024-12-12 Published:2025-04-12 Published online:2024-12-19
  • Contact: E-mail: lishaoxiong@gdaas.cn; E-mail: luqing@gdaas.cn
  • Supported by:
    National Natural Science Foundation of China(32172051);National Natural Science Foundation of China(32301869);China Agriculture Research System of MOF and MARA(CARS-13);National Key R&D Program of China(2023YFD1202800);Special Funds for the Revitalization of Agriculture through Seed Industry under the Provincial Rural Revitalization Strategy(2024);Guangdong Provincial Key Research and Development Program-Modern Seed Industry(2022B0202060004);Guangdong Basic and Applied Basic Research Foundation(2023A1515010098);Guangdong Basic and Applied Basic Research Foundation(2024A1515010511)

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摘要：

花生(Arachis hypogaea L.)是我国重要的经济作物和油料作物, 其荚果大小与单株产量紧密联系, 是重要的农艺性状。本研究以大果地方品种“东莞半蔓(DB)”和小果材料“ZLA”杂交构建的RIL群体为材料, 利用花生10K液相芯片构建高密度遗传图谱, 结合4个种植环境下的荚果大小(荚果长、荚果宽、荚果厚和百果重)相关性状进行QTL定位。总共检测到30个QTL, 分布在A01、A03、A05、A06、A07、A08、B02、B04、B06和B10等10条染色体上, LOD值为4.04~34.17, 贡献率为3.10%~33.52%, 加性效应为-2.43~16.64。检测到13个与荚果长、荚果宽、荚果厚和百果重有关的主效QTL, LOD值为4.41~34.17, 贡献率为11.21%~33.52%。在这些主效QTL中, qPLA07在4个种植环境下均被稳定检测到, qPWA08.1、qPWB02、qPTB06在3个种植环境下均被稳定检测到。另外, 检测到14对上位性QTL, LOD值为5.07~6.67, PVE为4.21%~21.84%。对qPWA08.1、qPWB02、qPTB06定位区间内的基因进行了KEGG代谢通路富集, 结合基因功能注释和花生不同组织中基因表达分析, 预测了4个候选基因, 分别是Ahy_A08g039622、Ahy_B02g057642、Ahy_B06g085859和Ahy_B06g085890。该研究结果有望为花生荚果产量关键基因挖掘和分子标记开发提供参考。

关键词: 花生, 荚果, QTL, 候选基因

Abstract:

Peanut (Arachis hypogaea L.) is an important economic and oilseed crop in China, with pod traits playing a critical role in determining yield. In this study, a recombinant inbred line (RIL) population derived from a cross between the large-pod local variety “Dongguan Banman (DB)” and the small-pod variety “ZLA” was used to construct a high-density genetic map with single nucleotide polymorphism (SNP) markers. This map was employed to identify quantitative trait loci (QTL) associated with pod traits across four distinct cultivation environments. A total of 30 QTLs were mapped to chromosomes A01, A03, A05, A06, A07, A08, B02, B04, B06, and B10, with logarithm of odds (LOD) values ranging from 4.04 to 34.17 and contribution rates from 3.10% to 33.52%. Among these, 13 major QTLs were associated with pod length, width, thickness, and 100-pod weight, showing LOD values between 4.41 and 34.17 and contribution rates between 11.21% and 33.52%. Notably, qPLA07 was consistently detected across all four environments, while qPWA08.1, qPWB02, and qPTB06 were stable in three environments. Additionally, 14 epistatic QTLs were identified, with LOD values ranging from 5.07 to 6.67 and phenotypic variation explained (PVE) from 4.21% to 21.84%. KEGG pathway enrichment analysis of genes within the QTL regions of qPWA08.1, qPWB02, and qPTB06 identified four candidate genes: Ahy_A08g039622, Ahy_B02g057642, Ahy_B06g085859, and Ahy_B06g085890, based on gene functional annotation and expression analysis across peanut tissues. These findings provide a theoretical foundation for identifying key genes regulating peanut pod yield and for developing molecular markers to facilitate breeding programs.

Key words: peanut, pod, QTL, candidate genes

图1

荚果表型图 RIL: 重组自交系。"

表1

亲本及RIL群体的描述性统计分析结果"

性状
Trait		 环境
Environment		 亲本 Parent RIL群体 RIL population
ZLA 东莞半蔓
Dongguan
Banman		 最大值
Max.		 最小值
Min.		 变异系数
CV (%)		 标准差
SD		 平均值
Mean		 偏度
Skewness		 峰度
Kurtosis
荚果长
PL (mm)		 E1 0.65 0.74** 52.57 23.30 0.18 6.13 33.40 0.695 0.480
E2 0.58 0.68** 42.09 22.16 0.14 4.35 32.21 -0.046 -0.416
E3 0.63 0.69** 53.04 23.63 0.17 5.81 34.51 0.673 0.491
E4 0.51 0.72** 50.59 21.23 0.16 5.07 32.37 0.560 1.009
荚果宽
PW (mm)		 E1 0.61 0.82** 19.20 10.22 0.13 1.84 14.53 0.192 -0.004
E2 0.57 0.95** 18.76 8.76 0.16 2.10 13.40 0.370 -0.292
E3 0.60 0.63** 22.31 9.46 0.14 1.96 14.02 0.489 0.787
E4 0.53 0.87** 17.64 9.41 0.13 1.76 13.33 -0.005 -0.336
荚果厚
PT (mm)		 E1 0.49 0.78** 18.98 9.69 0.13 1.91 14.25 0.166 -0.189
E2 0.42 0.69** 20.23 8.73 0.16 2.09 12.91 0.871 0.392
E3 0.55 0.81** 19.59 9.04 0.13 1.82 13.82 -0.016 0.218
E4 0.34 0.82** 16.91 8.91 0.12 1.62 13.52 -0.226 -0.353
百果重
HPW (mm)		 E1 5.68 4.97** 314.00 61.40 0.29 44.96 155.85 0.583 0.024
E2 5.41 3.42** 227.00 63.00 0.29 37.60 130.54 0.257 -0.419
E3 4.32 3.01** 296.00 56.00 0.28 47.12 167.34 0.414 0.166
E4 4.26 5.51** 212.00 52.00 0.29 35.65 123.53 0.359 -0.225

表2

4个环境下各性状的相关性分析结果"

环境Environment 性状Trait 荚果长PL 荚果宽PW 荚果厚PT
E1 荚果宽PW 0.349***
荚果厚PT 0.302*** 0.914***
百果重HPW 0.636*** 0.774*** 0.768***
E2 荚果宽PW 0.373***
荚果厚PT 0.363*** 0.854***
百果重HPW 0.532*** 0.788*** 0.670***
E3 荚果宽PW 0.171***
荚果厚PT 0.240*** 0.856***
百果重HP图W 0.574*** 0.610*** 0.697***
E4 荚果宽PW 0.312***
荚果厚PT 0.482*** 0.883***
百果重HPW 0.524*** 0.731*** 0.705***

图2

4个环境下RIL群体不同性状的频率分布图 缩写同表1。Abbreviations are the same as those given in Table 1."

表3

花生荚果相关性状QTL分析结果"

性状
Trait		 位点
QTL		 环境
Environment		 染色体
Chr.		 标记区间
Marker interval		 LOD 贡献率
PVE (%)		 加性效应
Additive
effect		 置信区间
Confidence interval
荚果长
PL (mm)		 qPLA01 E2 A01 A01_11204930-11352342 7.0403 15.2310 -1.8397 37.5-40.5
qPLA05 E2 A05 A05_8652005-11538045 4.5490 11.2089 -1.5964 192.0-203.5
qPLA06 E1 A06 A06_1765658-3081683 4.6951 8.7442 1.9602 0-8.5
qPLA07 E1 A07 A07_166832022-166955022 14.6721 31.2684 3.7220 488.5-491.0
E2 A07 9.1447 21.7858 2.2249 486.5-491.0
E3 A07 5.9719 16.2443 2.4481 484.5-491.0
E4 A07 6.3490 17.2817 2.1865 487.5-491.0
荚果宽
PW (mm)		 qPWA03 E4 A03 A03_143317504-144635493 4.9992 9.3638 0.5257 354.0-363.0
qPWA06 E4 A06 A06_115549348-115817873 4.4243 7.9380 0.4776 197.0-199.0
qPWA08.1 E1 A08 A08_30048499-30366347 6.0062 15.6656 0.7732 64.5-65.5
E2 A08 7.6455 21.6332 0.9226 65.5-67.5
E4 A08 5.6550 10.5400 0.5522 65.5-67.5
qPWA08.2 E3 A08 A08_37177561-37928646 6.1705 3.3958 0.7702 77.5-78.5
qPWB02 E2 B02 B02_4887376-5205416
B02_5205416-6387357		 6.0087 16.2445 0.8084 34.5-38.5
E3 B02 5.8390 3.0950 0.7437 34.5-37.5
E4 B02 6.6999 13.4146 0.6311 34.5-38.5
qPWB06 E1 B06 B06_138639856-140196491 5.9124 15.4844 0.7643 48.5-49.5
qPWB10 E3 B10 B10_33405033-32604657 34.1719 33.5202 -2.4344 63.5-64.5
荚果厚
PT (mm)		 qPTA03 E4 A03 A03_143317504-144635493 4.1054 9.5411 0.4756 354-362.0
qPTA08 E4 A08 A08_30048499-30366347 4.2747 9.9395 0.4815 64.5-65.5
E1 A08 8.2452 15.9256 0.8437 65.5-66.5
qPTB02 E1 B02 B02_4887376-5205416 8.3107 15.8808 0.8525 34.5-37.5
qPTB04 E1 B04 B04_127248538-126884743 4.9720 9.6182 0.7093 88.5-89.0
qPTB06 E2 B06 B06_146907751-148783006 6.6930 18.5502 0.9310 70.5-77.0
E3 B06 4.2572 14.1986 0.6975 70.5-77.0
E4 B06 5.8566 15.7462 0.4526 71.5-77.0
百果重
HPW (g)		 qHPWA03.1 E1 A03 A03_141234947-141092590 4.9493 14.1606 16.6366 339.0-342.0
qHPWA03.2 E2 A03 A03_139238268-139848157 6.7751 12.7953 15.2542 321.0-325.0
qHPWA06 E2 A06 A06_113190229-113520763 4.0418 7.0298 11.1996 185.0-192.0
qHPWB10 E1 B10 B10_145433611-145968886 4.4101 11.7996 14.5291 174.0-184.0

图3

花生荚果相关性状QTL定位结果 缩写同表1。"

表4

花生荚果相关性状上位性QTL定位结果"

性状
Trait		 环境
Environment		 上位性QTL
E-QTL		 染色体
Chr.		 位置1
Pos. 1		 标记区间1
Marker interval 1		 上位性QTL
E-QTL		 染色体
Chr.		 位置2
Pos. 2		 标记区间2
Marker interval 2		 LOD 贡献率
PVE (%)
荚果长
PL
(mm)		 E3 E-qPLA03 A03 0 A03_71003-621044 E-qPLB04 B04 5 B04_1300271-2726314 5.40 21.84
E4 E-qPLA05 A05 210 A05_16823212-17149189 E-qPLB10 B10 205 B10_148392050-148148634 6.67 15.98
荚果宽
PW
(mm)		 E1 E-qPWB04 B04 30 B04_4064597-8111568 E-qPWB05 B05 70 B05_28723528-31732034 5.39 16.03
E1 E-qPWA08 A08 65 A08_29556435-29781487 E-qPWB08 B08 65 B08_126197151-126599602 5.36 16.70
E2 E-qPWA04.1 A04 145 A04_108410606-108792245 E-qPWA07 A07 470 A07_164614645-164794252 5.12 13.85
E3 E-qPWA04.2 A04 145 A04_108410606-108792245 E-qPWA08 A08 40 A08_9856553-10239337 6.24 16.11
荚果厚
PT
(mm)		 E1 E-qPTA04 A04 145 A04_108410606-108792245 E-qPTA07 A07 470 A07_164614645-164794252 5.99 19.36
E2 E-qPTA09 A09 115 A09_75588894-106054640 E-qPTA10 A10 125 A10_3847294-4076607 5.50 4.40
E2 E-qPTA08 A08 65 A08_29556435-29781487 E-qPTB01.1 B01 75 B01_31459252-41455928 6.33 5.01
E2 E-qPTA10 A10 125 A10_3847294-4076607 E-qPTB02.2 B01 75 B01_31459252-41455928 5.46 4.49
E2 E-qPTB01.1 B01 70 B01_31459252-41455928 E-qPTB04 B04 60 B04_77304078-87562376 5.07 4.33
E2 E-qPTB01.2 B01 75 B01_31459252-41455928 E-qPTB09 B09 80 B09_155190824-158481352 5.26 4.21
百果重
HPW
(g)		 E3 E-qHPWA03 A03 0 A03_71003-621044 E-qHPWA05 A05 240 A05_28575794-29060303 6.47 18.17
E3 E-qHPWB02 B02 165 B02_34558390-102335914 E-qHPWAB08 B08 10 B08_2544346-2638685 5.24 13.54

图4

qPWA08.1, qPWB02和qPTB06区间候选基因KEGG通路富集分析"

表5

3个QTL的候选基因分析"

基因ID
Gene ID		 染色体
Chr.		 标记区间
Marker interval (bp)		 基因家族
Gene family		 基因功能注释
Gene functional description
Ahy_A08g039614 A08 30126461-30179893 legfed_v1_0.L_8Q8YMG 自噬相关蛋白8 Autophagy protein 8
Ahy_A08g039622 A08 30271630-30271880 legfed_v1_0.L_56M8PD 热休克蛋白90 Heat shock protein 90
Ahy_A08g039624 A08 30283347-30291196 legfed_v1_0.L_2H8YNS 顺乌头酸酶Aconitase
Ahy_B02g057589 B02 4893488-4896861 legfed_v1_0.L_Q5KQS5 吡哆胺-5'-磷酸氧化酶
Pyridoxamine 5'-phosphate oxidase
Ahy_B02g057608 B02 5171380-5171736 legfed_v1_0.L_9WDQD0 EF手型结构域钙结合蛋白
EF-hand calcium-binding proteins
Ahy_B02g057640 B02 5652666-5658241 legfed_v1_0.L_29W3YK 丝氨酸/苏氨酸蛋白激酶
Serine/Threonine kinase proteins
Ahy_B02g057642 B02 5756798-5758215 legfed_v1_0.L_KCL7Q5 b HLH转录因子
Basic helix-loop-helix transcription factor
Ahy_B02g057660 B02 5907035-5918712 legfed_v1_0.L_0C0SD2 BRO 1结构域蛋白
BRO domain-containing protein 1
Ahy_B02g057673 B02 6069768-6073611 legfed_v1_0.L_1GQHGD 3-酮酯酰-CoA合酶
3-ketoacyl-CoA synthases
Ahy_B06g085840 B06 147106411-147106976 legfed_v1_0.L_0JZZ84 聚酮环化酶2 Polyketide cylcases 2
Ahy_B06g085859 B06 147357241-147378643 legfed_v1_0.L_5MH5QP 早花3转录因子Early flowering 3
Ahy_B06g085890 B06 147787935-148593101 legfed_v1_0.L_YFP2RZ AP2类乙烯反应转录因子
AP2-like ethylene-responsive transcription factor

图5

QTL中候选基因在花生不同组织的差异表达"

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