水稻抽穗期QTL定位及候选基因分析

doi:10.11983/CBB22114

植物学报 ›› 2022, Vol. 57 ›› Issue (5): 588-595.DOI: 10.11983/CBB22114

水稻抽穗期QTL定位及候选基因分析

魏和平¹^,^†, 芦涛²^,^†, 贾绮玮², 邓飞³, 朱浩³, 岂泽华¹, 王玉玺¹, 叶涵斐², 殷文晶², 方媛², 穆丹¹^,^*(), 饶玉春²^,^*()

¹安庆师范大学生命科学学院, 安庆市林业科技创新研究院, 皖西南生物多样性研究与生态保护安徽省重点实验室, 安庆 246133
²浙江师范大学化学与生命科学学院, 金华 321004
³金华市农业科学研究院, 金华 321051

收稿日期:2022-05-31 接受日期:2022-07-25 出版日期:2022-09-01 发布日期:2022-09-09
通讯作者: 穆丹,饶玉春
作者简介:ryc@zjnu.cn
*E-mail: mudansmile@126.com;
第一联系人：^†共同第一作者
基金资助:
安徽省软科学研究计划(12020503c089);林业科技攻关配套服务项目(604-20065);树形月季及五彩月季集成技术研发与示范(604-210042);安庆市林业科技创新研究院林木育种实验室建设(604-210086);安徽省生命科学实验实训中心、安徽省园林专业结构优化调整与专业改造、安徽省园林专业实验实训中心(2015sxzx014);皖西南生物多样性研究与生态保护安徽省重点实验室开放基金(Wz2021002);皖西南生物多样性研究与生态保护安徽省重点实验室开放基金(Wsz202207);皖西南生物多样性研究与生态保护安徽省重点实验室开放基金(Wy202206);安庆师范大学研究生教育教学改革项目(2021aqnujyxm64)

QTL Mapping of Candidate Genes for Heading Date in Rice

Wei Heping¹^,^†, Lu Tao²^,^†, Jia Qiwei², Deng Fei³, Zhu Hao³, Qi Zehua¹, Wang Yuxi¹, Ye Hanfei², Yin Wenjing², Fang Yuan², Mu Dan¹^,^*(), Rao Yuchun²^,^*()

¹The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing Academy of Forestry Science and Technology, School of Life Sciences, Anqing Normal University, Anqing 246133, China
²College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
³Jinhua Academy of Agricultural Sciences, Jinhua 321051, China

Received:2022-05-31 Accepted:2022-07-25 Online:2022-09-01 Published:2022-09-09
Contact: Mu Dan,Rao Yuchun
About author:ryc@zjnu.cn
*E-mail: mudansmile@126.com;
First author contact:^†These authors contributed equally to this paper

摘要/Abstract

摘要： 水稻(Oryza sativa)抽穗期是决定产量和品质的重要性状, 在育种、制种及引种驯化过程中发挥重要作用。将热研2号(O. sativa subsp. japonica cv. ‘Nekken2’)和华占(O. sativa subsp. indica cv. ‘HZ’)杂交获得F₁代, 经连续多代自交得到120个重组自交系(RILs)群体。在常规水肥管理条件下, 对120个RILs株系的抽穗时间进行统计分析。利用已构建好的高密度遗传图谱, 对水稻抽穗期相关性状进行QTL定位分析, 结果共检测到11个QTLs, 分别位于第1、3、4、5、6、8和12号染色体上, 其中1个LOD值高达5.75。通过分析QTLs区间内的候选基因, 筛选出可能影响两亲本抽穗期的相关基因, 并利用实时定量PCR进行基因表达量分析, 发现LOC_Os03g03070、LOC_Os03g50310、LOC_Os03g55389、LOC_Os04g55510、LOC_Os08g07740和LOC_Os08g01670共6个基因在双亲间的表达量差异显著, 其中LOC_Os03g50310在Nekken2中的表达量比HZ高3.6倍。对双亲间候选基因LOC_Os03g50310进行测序分析, 发现该基因在5′UTR、CDS区及3′UTR存在4处差异, 其中CDS区的单核苷酸多态性(SNP)差异引发单个氨基酸改变。研究通过挖掘水稻抽穗期QTL位点为进一步克隆水稻抽穗期相关基因和品种选育提供了新线索。

关键词: 水稻, 抽穗期, QTL定位, 候选基因, 单核苷酸多态性

Abstract: The heading date is an important trait that determines the yield and quality of rice, and plays an important role in the process of rice breeding, seed production, introduction and domestication. In this study, F₁ was obtained by a cross between Nekken2 (Oryza sativa subsp. japonica cv. ‘Nekken2’) and Huazhan (O. sativa subsp. indica cv. ‘HZ’), and 120 recombination inbred lines (RILs) were obtained through successive multi-generational selfing. The population of RILs was used as experimental material. Under the condition of conventional water and fertilizer management, the time of heading stage of 120 lines was analyzed. Using the high-density genetic map constructed by this population, the QTLs for the heading date was mapped and analyzed. A total of 11 QTLs were detected on chromosomes 1, 3, 4, 5, 6, 8, and 12, respectively, and one of the LOD values was as high as 5.75. By analyzing the candidate genes in the QTLs interval, the related genes that may affect the heading date were screened out, and real-time quantitative PCR was used for gene expression analysis. The expression levels of six genes, LOC_Os03g03070, LOC_Os03g50310, LOC_Os03g55389, LOC_Os04g55510, LOC_Os08g07740, and LOC_Os08g01670 significantly different between parents, and the expression of LOC_Os03g50310 in Nekken2 was 3.6 times higher than that in HZ. In addition, the sequencing analysis showed that there were 4 differences in the 5'UTR, CDS region and 3'UTR of the candidate gene LOC_Os03g50310 between the parents, of which the single nucleotide polymorphisms (SNP) difference in the CDS region caused a single amino acid change. This study provides new clues for further cloning of heading date-related genes and cultivar selection by mining the QTL loci related to heading date in rice.

Key words: rice, heading date, QTL mapping, candidate genes, single nucleotide polymorphisms (SNP)

魏和平, 芦涛, 贾绮玮, 邓飞, 朱浩, 岂泽华, 王玉玺, 叶涵斐, 殷文晶, 方媛, 穆丹, 饶玉春. 水稻抽穗期QTL定位及候选基因分析. 植物学报, 2022, 57(5): 588-595.

Wei Heping, Lu Tao, Jia Qiwei, Deng Fei, Zhu Hao, Qi Zehua, Wang Yuxi, Ye Hanfei, Yin Wenjing, Fang Yuan, Mu Dan, Rao Yuchun. QTL Mapping of Candidate Genes for Heading Date in Rice. Chinese Bulletin of Botany, 2022, 57(5): 588-595.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB22114

https://www.chinbullbotany.com/CN/Y2022/V57/I5/588

图/表 8

参考文献 32

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Primer name	Forward primer (5′-3′)	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os03g50310	AGCAGCAGATCGAGCAGAAG	CTTCTCGTCGTCCAAGAAGC
LOC_Os03g55389	TGTCAAGCCCCACAATGTTA	AAGGCTCCACATGTCCAAAG
LOC_Os03g57940	AGCACCGAAGCAGTAAAGGA	AAGCAACCATATGGGCAGAC
LOC_Os03g03070	AAAAGCTGACGCTGATGGTT	TCCTTCCCCTGATGCTAATG
LOC_Os04g55510	GTGGCCTAAGGATTGGTGAA	TGAGAGCAGCCACCATGTAG
LOC_Os08g07740	GGAAGAGCTATGGGCACTTG	CGACTCCTTGGAGATCTTGG
LOC_Os08g01420	GACAGGTCTAGCGAGCAACC	GGCACAGTTCGTTTCGGTAT
LOC_Os08g01670	GATGGGGCAGCAGGACTAC	GATGCAGGAGAGGAGGTGAG

Primer name	Forward primer (5′-3′)	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os03g50310	AGCAGCAGATCGAGCAGAAG	CTTCTCGTCGTCCAAGAAGC
LOC_Os03g55389	TGTCAAGCCCCACAATGTTA	AAGGCTCCACATGTCCAAAG
LOC_Os03g57940	AGCACCGAAGCAGTAAAGGA	AAGCAACCATATGGGCAGAC
LOC_Os03g03070	AAAAGCTGACGCTGATGGTT	TCCTTCCCCTGATGCTAATG
LOC_Os04g55510	GTGGCCTAAGGATTGGTGAA	TGAGAGCAGCCACCATGTAG
LOC_Os08g07740	GGAAGAGCTATGGGCACTTG	CGACTCCTTGGAGATCTTGG
LOC_Os08g01420	GACAGGTCTAGCGAGCAACC	GGCACAGTTCGTTTCGGTAT
LOC_Os08g01670	GATGGGGCAGCAGGACTAC	GATGCAGGAGAGGAGGTGAG

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
qhd-1	1	25257953-25481977	108.27-109.23	3.75
qhd-3	3	13767411-14882947	54.53-63.79	3.82
qhd-4	3	15628988-15779451	66.72-67.64	3.09
qhd-5	3	17197291-17357469	73.72-74.40	3.33
qhd-6	3	28536151-33494350	122.32-143.58	4.87
qhd-7	4	2572479-3906500	11.02-16.74	3.17
qhd-8	4	31066905-34944379	133.17-149.79	5.75
qhd-9	5	26262798-26850392	112.58-115.10	3.14
qhd-10	6	4227455-4659759	18.12-19.97	3.97
qhd-11	8	3480879-4936569	18.12-19.97	5.06
qhd-12	12	26219257-27272729	112.39-116.97	3.98

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
qhd-1	1	25257953-25481977	108.27-109.23	3.75
qhd-3	3	13767411-14882947	54.53-63.79	3.82
qhd-4	3	15628988-15779451	66.72-67.64	3.09
qhd-5	3	17197291-17357469	73.72-74.40	3.33
qhd-6	3	28536151-33494350	122.32-143.58	4.87
qhd-7	4	2572479-3906500	11.02-16.74	3.17
qhd-8	4	31066905-34944379	133.17-149.79	5.75
qhd-9	5	26262798-26850392	112.58-115.10	3.14
qhd-10	6	4227455-4659759	18.12-19.97	3.97
qhd-11	8	3480879-4936569	18.12-19.97	5.06
qhd-12	12	26219257-27272729	112.39-116.97	3.98

Chromosome	Gene name	Function
3	LOC_Os03g50310	Regulation of rice blast resistance through salicylic acid and ethylene signaling pathways, mediating heading stage
3	LOC_Os03g55389	Delaying flowering time by inhibiting the expression of FT-like genes
3	LOC_Os03g57940	Negative regulation of gibberellin signaling by phosphorylating the DELLA protein SLR1
3	LOC_Os03g03070	Involved in the regulation of adventitious root formation in rice by regulating auxin transport
4	LOC_Os04g55510	Mediates ubiquitination to degrade Hd1 through a 26S proteasome-mediated pathway
8	LOC_Os08g07740	Controlling the yield, plant height and heading date of rice
8	LOC_Os08g01420	Induction of rice heading by inhibiting Ghd7
8	LOC_Os08g01670	Regulation of pectin methyl esterification levels

水稻抽穗期QTL定位及候选基因分析

QTL Mapping of Candidate Genes for Heading Date in Rice

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