欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (5): 1400-1408.doi: 10.3724/SP.J.1006.2025.44145

• 研究简报 • 上一篇    

花生开花时间的全基因组关联分析及候选基因筛选

李文佳1,2,廖泳俊2,黄璐2,鲁清2,李少雄2,陈小平2,金晶炜1,*,王润风2,*   

  1. 1 西北农林科技大学草业与草原学院, 陕西杨凌712100; 2 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
  • 收稿日期:2024-09-04 修回日期:2024-12-12 接受日期:2024-12-12 出版日期:2025-05-12 网络出版日期:2024-12-19
  • 通讯作者: 王润风, E-mail: wangrunfeng@gdaas.cn; 金晶炜, E-mail: jinjingweisoil2008@163.com
  • 基金资助:
    本研究由广州市基础与应用基础研究项目(2023A04J0776)，广东省农业科学院农业优势产业学科团队项目(202104TD)和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)资助。

Genome-wide associate analysis of flowering traits and identification of candidate genes in peanut

LI Wen-Jia1,2,LIAO Yong-Jun2,HUANG Lu2,LU Qing2,LI Shao-Xiong2,CHEN Xiao-Ping2,JIN Jing-Wei1,*,WANG Run-Feng2,*   

  1. 1 College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China; 2 Crops Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Provincial Key Laboratory of Crop Genetic Improvement / South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou 510640, Guangdong, China
  • Received:2024-09-04 Revised:2024-12-12 Accepted:2024-12-12 Published:2025-05-12 Published online:2024-12-19
  • Contact: 王润风, E-mail: wangrunfeng@gdaas.cn; 金晶炜, E-mail: jinjingweisoil2008@163.com
  • Supported by:
    This study was supported by the Guangzhou Basic and Applied Basic Research Foundation (2023A04J0776), the Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences (202104TD), and the China Agriculture Research System of MOF and MARA (CARS-13).

PDF

70

摘要：

开花时间是评价花生早熟品种的重要指标之一，对产量亦有重要影响。挖掘花生开花时间相关遗传位点并筛选候选基因，对于花生早熟育种至关重要。本文以390份花生栽培种自然群体为材料，统计了在5种环境下的开花时间。表型统计结果显示，5种环境下，花生开花时间的变异系数介于3.21%~8.54%之间，存在较丰富的表型变异。花生的开花时间基本呈现正态分布，且受环境影响较大。通过全基因组关联分析，共得到259个与开花时间显著关联的SNP位点，其中有29个位点在2个以上环境中重复出现，分别位于A01、A02、A03、A04、A05、A07、A10、B01、B02、B03、B04、B06、B07、B09染色体上，可解释3.47%~8.58%的表型变异。在29个重复出现位点上下游100 kb的置信区间寻找候选基因，共发现159个有功能注释的基因。在重复检测的位点的候选区间中预测到7个与花生开花时间相关的候选基因，分别编码R2R3-MYB转录因子、叶绿素a-b结合蛋白、bHLH转录因子、WRKY转录因子、FAR1转录因子。研究结果可为解析花生开花调控遗传机制及花生早熟育种奠定基础。

关键词: 花生, 开花时间, 全基因组关联分析, 候选基因

Abstract:

The flowering time, one of the important indexes to evaluate the early maturing varieties of peanut, has an important impact on the yield. It is very important to mine the genetic loci related to peanut flowering time and screen candidate genes for early maturation breeding of peanut. In this paper, the flowering time of 390 peanut germplasms in five environments was evaluated. Phenotypic statistics showed that the variation coefficient of peanut flowering time ranged from 3.21% to 8.54% in five environments, and there were abundant phenotypic variations. The flowering time of peanut basically showed normal distribution and was greatly affected by the environment. A total of 259 SNPs significantly associated with flowering time were identified by genome-wide association analysis. Of them, 29 were identified in more than two environments, and located on chromosomes A01, A02, A03, A04, A05, A07, A10, B01, B02, B03, B04, B06, B07, and B09, it can explain 3.47% to 8.58% of the phenotypic variation. After searching for candidate genes in the confidence intervals of 29 recurrent loci upstream and downstream 100 kb, 159 genes with functional annotations were found. Seven candidate genes related to peanut flowering time were predicted in the candidate interval, encoding R2R3-MYB transcription factor, chlorophyll a-b binding protein, bHLH transcription factor, WRKY transcription factor and FAR1 transcription factor, respectively. The results of this study can lay a foundation for understanding the genetic mechanism of peanut flowering regulation and peanut early maturation breeding.

Key words: peanut, flowering time, genome-wide association analysis, candidate gene

[1] 刘珂珂, 郭峰, 杨莎, 王建国, 高华鑫, 邹洁, 张佳蕾, 万书波. “二次镇压”对花生子叶节的出土调控增产效果. 中国油料作物学报, 网络首发[2024-04-11], https://link.cnki.net/doi/10.19802/j.issn.1007-9084.2023265.

Liu K K, Guo F, Yang S, Wang J G, Gao H X, Zou J, Zhang J L, Wan S B. “Second suppression” on peanut cotyledon festival. Chin J Oil Crop Sci, Published online [2024-04-11], https://link.cnki.net/doi/10.19802/j.issn.1007-9084.2023265 (in Chinese with English abstract).

[2] 田永国, 胡廷会, 丁广刚, 成良强, 饶庆琳, 姜敏, 王金花, 吕建伟, 王军. 花生荚果发育和成熟阶段的秸秆品质变化分析. 花生学报, 2023, 52(2): 91–95.

Tian Y G, Hu T H, Ding G G, Cheng L Q, Rao Q L, Jiang M, Wang J H, Lyu J W, Wang J. Analysis on dynamics of peanut straw quality at pod developmental and harvesting stages. J Peanut Sci, 2023, 52(2): 91–95 (in Chinese with English abstract). 

[3] Upadhyaya H D, Nigam S N. Inheritance of two components of early maturity in groundnut (Arachis hypogaea L.). Euphytica, 1994, 78: 59–67.

[4] Irish V F. The flowering of Arabidopsis flower development. Plant J, 2010, 61: 1014–1028. 

[5] Lin X Y, Liu B H, Weller J L, Abe J, Kong F J. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. J Integr Plant Biol, 2021, 63: 981–994. 

[6] 曹永策, 李曙光, 张新草, 孔杰杰, 赵团结. 夏大豆重组自交系群体遗传图谱构建及开花期QTL分析. 中国农业科学, 2020, 53: 683–694.

Cao Y C, Li S G, Zhang X C, Kong J J, Zhao T J. Construction of genetic map and mapping QTL for flowering time in A summer planting soybean recombinant inbred line population. Sci Agric Sin, 2020, 53: 683–694 (in Chinese with English abstract). 

[7] Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol, 2012, 12: 80.

[8] 李华东, 杨会, 吕玉英, 张秀荣, 张昆, 刘风珍, 万勇善. 栽培花生花期相关QTL定位. 山东农业科学, 2021, 53(2): 1–6.

Li H D, Yang H, Lyu Y Y, Zhang X R, Zhang K, Liu F Z, Wan Y S. QTL mapping for flowering time in cultivated peanut (Arachis hypogaea L.). Shandong Agric Sci, 2021, 53(2): 1–6 (in Chinese with English abstract). 

[9] Zhong C, Li Z, Cheng Y L, Zhang H N, Liu Y, Wang X G, Jiang C J, Zhao X H, Zhao S L, Wang J, Zhang H, Liu X B, Yu H Q. Comparative genomic and expression analysis insight into evolutionary characteristics of PEBP genes in cultivated peanuts and their roles in floral induction. Int J Mol Sci, 2022, 23: 12429.

[10] Wang L, Yang X L, Cui S L, Zhao N N, Li L, Hou M Y, Mu G J, Liu L F, Li Z C. High-density genetic map development and QTL mapping for concentration degree of floret flowering date in cultivated peanut (Arachis hypogaea L.). Mol Breed, 2020, 40: 17.

[11] 杨飞, 张征锋, 南波, 肖本泽. 水稻产量相关性状的全基因组关联分析及候选基因筛选. 作物学报, 2022, 48: 1813–1821.

Yang F, Zhang Z F, Nan B, Xiao B Z. Genome-wide association analysis and candidate gene selection of yield related traits in rice. Acta Agron Sin, 2022, 48: 1813–1821 (in Chinese with English abstract). 

[12] 彭小爱, 卢茂昂, 张玲, 刘童, 曹磊, 宋有洪, 郑文寅, 何贤芳, 朱玉磊. 基于55K SNP芯片的小麦籽粒主要品质性状的全基因组关联分析. 作物学报, 2024, 50: 1948–1960.

Peng X A, Lu M A, Zhang L, Liu T, Cao L, Song Y H, Zheng W Y, He X F, Zhu Y L. Genome-wide association study of major grain quality traits in wheat based on 55K SNP arrays. Acta Agron Sin, 2024, 50: 1948–1960 (in Chinese with English abstract). 

[13] 杨豪, 向仕华, 刘丽, 宁可君, 杨雪, 舒英杰, 何庆元. 川渝大豆生育期性状的全基因组关联分析. 作物学报, 2023, 49: 2727–2737.

Yang H, Xiang S H, Liu L, Ning K J, Yang X, Shu Y J, He Q Y. Genome-wide association analysis of growth period traits in soybean of Sichuan and Chongqing. Acta Agron Sin, 2023, 49: 2727–2737 (in Chinese with English abstract).

[14] Long Y, Shi J, Qiu D, Li R, Zhang C, Wang J, Hou J, Zhao J, Shi L, Park B S, Choi S R, Lim Y P, Meng J. Flowering time quantitative trait Loci analysis of oilseed Brassica in multiple environments and genome wide alignment with Arabidopsis. Genetics, 2007, 177: 2433–2444. 

[15] 黄吉祥, 熊化鑫, 潘兵, 倪西源, 张晓玉, 赵坚义. 油菜开花期QTL定位及与粒重的遗传关联性. 中国农业科学, 2016, 49: 3073–3083.

Huang J X, Xiong H X, Pan B, Ni X Y, Zhang X Y, Zhao J Y. Mapping QTL of flowering time and their genetic relationships with seed weight in Brassica napus. Sci Agric Sin, 2016, 49: 3073–3083 (in Chinese with English abstract). 

[16] Chen X P, Lu Q, Liu H, Zhang J N, Hong Y B, Lan H F, Li H F, Wang J P, Liu H Y, Li S X, Pandey M K, Zhang Z K, Zhou G Y, Yu J G, Zhang G Q, Yuan J Q, Li X Y, Wen S J, Meng F B, Yu S L, Wang X Y, Siddique K H M, Liu Z J, Paterson A H, Varshney R K, Liang X Q. Sequencing of cultivated peanut, Arachis hypogaea, yields insights into genome evolution and oil improvement. Mol Plant, 2019, 12: 920–934.

[17] Lu Q, Huang L, Liu H, Garg V, Gangurde S S, Li H F, Chitikineni A, Guo D D, Pandey M K, Li S X, Liu H Y, Wang R F, Deng Q Q, Du P X, Varshney R K, Liang X Q, Hong Y B, Chen X P. A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits. Nat Genet, 2024, 56: 530–540. 

[18] 梁晓艳, 付娆, 李佳佳, 衣葵花, 唐朝辉, 郭峰, 王建国, 张佳蕾, 万书波. 不同密度单粒精播对花生开花动态及结实特性的影响. 中国油料作物学报, 2024, 46: 450–459.

Liang X Y, Fu R, Li J J, Yi K H, Tang C H, Guo F, Wang J G, Zhang J L, Wan S B. Effect of different densities of single-seed sowing on flowering dynamics and fruiting characteristics of peanut. Chin J Oil Crop Sci, 2024, 46: 450–459 (in Chinese with English abstract). 

[19] 赵存花, 李俊庆, 张贵国. 旱地花生开花规律及有效花终止期的研究. 中国油料作物学报, 1998, 20(2): 52–54.

Zhao C H, Li J Q, Zhang G G. Studies on flowering habit and closing date for effective flower in dry-land peanut. Chin J Oil Crop Sci, 1998, 20: 52–54 (in Chinese with English abstract). 

[20] Fonceka D, Tossim H A, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn M C, Bertioli D J, Glaszmann J C, Courtois B, Rami J F. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biol, 2012, 12: 26. 

[21] Guo D S, Zhang J Z, Wang X L, Han X, Wei B Y, Wang J Q, Li B X, Yu H, Huang Q P, Gu H Y, Qu L J, Qin G J. The WRKY transcription factor WRKY71/EXB1 controls shoot branching by transcriptionally regulating RAX genes in Arabidopsis. Plant Cell, 2015, 27: 3112–3127. 

[22] Yang F, Wang Q, Schmitz G, Müller D, Theres K. The bHLH protein ROX acts in concert with RAX1 and LAS to modulate axillary meristem formation in Arabidopsis. Plant J, 2012, 71: 61–70. 

[23] 韩艺, 赵继发, 蔡璨, 彭疑芳, 张梅娟, 沙伟, 马天意. 光捕获叶绿素a/b结合蛋白基因在植物逆境胁迫中的研究进展. 高师理科学刊, 2023, 43(6): 79–83.

Han Y, Zhao J F, Cai C, Peng Y F, Zhang M J, Sha W, Ma T Y. Research progress of light-harvesting chlorophyll a/b-binding protein genes in plant stresses. J Sci Teach Coll Univ, 2023, 43(6): 79–83 (in Chinese with English abstract).

[24] Han X W, Han S, Li Y T, Li K K, Yang L J, Ma D F, Fang Z W, Yin J L, Zhu Y X, Gong S J. Double roles of light-harvesting chlorophyll a/b binding protein TaLhc2 in wheat stress tolerance and photosynthesis. Int J Biol Macromol, 2023, 253: 127215.

[25] Hao Y Q, Zong X M, Ren P, Qian Y Q, Fu A G. Basic helix-loop-helix (bHLH) transcription factors regulate a wide range of functions in Arabidopsis. Int J Mol Sci, 2021, 22: 7152.

[26] Ito S, Song Y H, Josephson-Day A R, Miller R J, Breton G, Olmstead R G, Imaizumi T. Flowering BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis. Proc Natl Acad Sci USA, 2012, 109: 3582–3587.

[27] 赵小波, 李春娟, 孙全喜, 王奇, 牟艺菲, 王娟, 苑翠玲, 姜常松, 单世华. 基于全基因组水平的花生FAR1转录因子家族分析. 花生学报, 2024, 53(2): 1–9.

Zhao X B, Li C J, Sun Q X, Wang Q, Mou Y F, Wang J, Yuan C L, Jiang C S, Shan S H. Genome-wide analysis of the FAR1 gene family in peanut. J Peanut Sci, 2024, 53(2): 1–9 (in Chinese with English abstract). 

[28] Lu Q, Liu H, Hong Y B, Liang X Q, Li S X, Liu H Y, Li H F, Wang R F, Deng Q Q, Jiang H F, Varshney R K, Pandey M K, Chen X P. Genome-wide identification and expression of FAR1 gene family provide insight into pod development in peanut (Arachis hypogaea). Front Plant Sci, 2022, 13: 893278.

[29] Ma L, Li G. FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) family proteins in Arabidopsis growth and development. Front Plant Sci, 2018, 9: 692.

[30] Li G, Siddiqui H, Teng Y B, Lin R C, Wan X Y, Li J G, Lau O S, Ou-Yang X H, Dai M Q, Wan J M, Devlin P F, Deng X W, Wang H Y. Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol, 2011, 13: 616–622. 

[31] Li D M, Fu X, Guo L, Huang Z G, Li Y P, Liu Y, He Z S, Cao X W, Ma X H, Zhao M C, Zhu G H, Xiao L T, Wang H Y, Chen X M, Liu R Y, Liu X G. FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. Proc Natl Acad Sci USA, 2016, 113: 9375–9380.

[32] 叶王斌, 王玲, 周晟, 杨娟, 刘桂伶, 范丽娟. 燕子花WRKY11基因克隆、结构分析及功能验证. 东北林业大学学报, 2023, 51(7): 1–9.

Ye W B, Wang L, Zhou S, Yang J, Liu G L, Fan L J. Cloning, structure analysis and functional verification of WRKY11 in iris laevigata. J Northeast For Univ, 2023, 51(7) 1–9 (in Chinese with English abstract).

[33] Zhang L P, Chen L G, Yu D Q. Transcription factor WRKY75 interacts with DELLA proteins to affect flowering. Plant Physiol, 2018, 176: 790–803. 

[34] 张雁明, 邢国芳, 刘美桃, 刘晓东, 韩渊怀. 全基因组关联分析: 基因组学研究的机遇与挑战. 生物技术通报, 2013, 29(6): 1–6.

Zhang Y M, Xing G F, Liu M T, Liu X D, Han Y H. Genome wide association study: opportunities and challenges in genomic research. Biotechnol Bull, 2013, 29(60): 1–6 (in Chinese with English abstract).

[35] 黄琼, 尹继业, 刘昭前. 2型糖尿病全基因组关联分析的研究进展. 中华内分泌代谢杂志, 2010, 26: 432–436.

Huang Q, Yin J Y, Liu Z Q. Progress of genome-wide association studies in type 2 diabetes mellitus. Chin J Endocrinol Metab, 2010, 26: 432–436 (in Chinese with English abstract).

[1] 张金泽, 周庆国, 肖莉晶, 金海润, 欧阳青静, 龙旭, 晏中彬, 田恩堂. 芥菜型油菜不同组织硫苷含量的QTL定位与候选基因分析[J]. 作物学报, 2025, 51(5): 1166-1177.
[2] 王亚雯, 戚正阳, 尤佳琦, 聂新辉, 曹娟, 杨细燕, 涂礼莉, 张献龙, 王茂军. 棉花60K功能位点基因芯片的制备及应用[J]. 作物学报, 2025, 51(5): 1178-1188.
[3] 林伟津, 郭泽佳, 刘浩, 李海芬, 王润风, 黄璐, 余倩霞, 陈小平, 洪彦彬, 李少雄, 鲁清. 花生荚果产量相关性状QTL定位与候选基因分析[J]. 作物学报, 2025, 51(4): 969-981.
[4] 迟晓元, 毕竞男, 赵健鑫, 陈娜, 潘丽娟, 姜骁, 殷祥贞, 赵旭红, 马俊卿, 许静. 花生荚果力学特性评鉴及早熟种质筛选[J]. 作物学报, 2025, 51(4): 943-957.
[5] 徐建霞, 丁延庆, 曹宁, 程斌, 高旭, 李文贞, 张立异. 中国高粱株高和节间数全基因组关联分析及候选基因预测[J]. 作物学报, 2025, 51(3): 568-585.
[6] 晋高锐, 吴小丽, 邓丽, 陈玉宁, 喻博伦, 郭建斌, 丁膺宾, 刘念, 罗怀勇, 陈伟刚, 黄莉, 周小静, 淮东欣, 谭家壮, 姜慧芳, 任丽, 雷永, 廖伯寿. 兼抗黄曲霉侵染和产毒高油酸花生新种质的创制与评价[J]. 作物学报, 2025, 51(3): 687-895.
[7] 金欣欣, 宋亚辉, 苏俏, 杨永庆, 李玉荣, 王瑾. 冀花系列高油酸花生抗旱性鉴定与综合评价[J]. 作物学报, 2025, 51(3): 797-811.
[8] 赵斐斐, 李少雄, 刘浩, 李海芬, 王润风, 黄璐, 余倩霞, 洪彦彬, 陈小平, 鲁清, 曹玉曼. 花生主茎节间和侧枝节间长度的关联作图及候选基因分析[J]. 作物学报, 2025, 51(2): 548-556.
[9] 胡朋举, 郭颂, 宋亚辉, 金欣欣, 苏俏, 杨永庆, 王瑾. 多环境下花生含油量遗传及QTL定位分析[J]. 作物学报, 2025, 51(2): 324-333.
[10] 郭淑慧, 潘转霞, 赵战胜, 杨六六, 皇甫张龙, 郭宝生, 胡晓丽, 录亚丹, 丁霄, 吴翠翠, 兰刚, 吕贝贝, 谭逢平, 李朋波. 陆地棉D11染色体一个纤维长度主效位点的遗传解析[J]. 作物学报, 2025, 51(2): 383-394.
[11] 王润风, 李文佳, 廖泳俊, 鲁清, 刘浩, 李海芬, 李少雄, 梁炫强, 洪彦彬, 陈小平. 花生核心种质资源荚果成熟度评鉴及早熟种质筛选[J]. 作物学报, 2025, 51(2): 395-404.
[12] 李嘉欣, 黄莹, 吴潞梅, 赵伦, 易斌, 马朝芝, 涂金星, 沈金雄, 傅廷栋, 文静. 甘蓝型油菜BnaSLY1基因进化分析及功能研究[J]. 作物学报, 2025, 51(1): 44-57.
[13] 马敏虎, 常华瑜, 陈朝燕, 仁增, 刘廷辉, 邢国芳, 郭刚刚. 苗草专用型大麦品种鉴定及全基因组关联分析[J]. 作物学报, 2025, 51(1): 91-102.
[14] 叶靓, 朱叶琳, 裴琳婧, 张思颖, 左雪倩, 李正真, 刘芳, 谭静. 联合全基因组关联和转录组分析筛选玉米拟轮枝镰孢穗腐病的抗性候选基因[J]. 作物学报, 2024, 50(9): 2279-2296.
[15] 禹海龙, 吴文雪, 裴星旭, 刘晓宇, 邓跟望, 李西臣, 甄士聪, 望俊森, 赵永涛, 许海霞, 程西永, 詹克慧. 小麦茎秆性状的转录组测序及全基因组关联分析[J]. 作物学报, 2024, 50(9): 2187-2206.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2