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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (10): 2633-2642.doi: 10.3724/SP.J.1006.2023.32007

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用双向导入系和重组自交系定位和挖掘水稻苗期耐冷QTL和有利等位基因

曹慧敏1,2(), 杨贤莉3(), 王立志3, 李苹苹1, 翟来圆2, 姜树坤3, 郑天清2, 邱先进1(), 徐建龙2,4,5()   

  1. 1农业农村部长江中游作物绿色高效生产重点实验室(省部共建), 长江大学农学院, 湖北荆州 434025
    2中国农业科学院作物科学研究所, 北京 100081
    3黑龙江省农业科学院耕作栽培研究所, 黑龙江哈尔滨 150086
    4岭南现代农业科学与技术广东省实验室深圳分中心, 中国农业科学院农业基因组研究所, 广东深圳 518210
    5海南省崖州湾种子实验室, 海南三亚 572024
  • 收稿日期:2023-02-16 接受日期:2023-04-17 出版日期:2023-10-12 网络出版日期:2023-04-24
  • 通讯作者: 邱先进, E-mail: xjqiu216@yangtzeu.edu.cn; 徐建龙, E-mail: xujianlong@caas.cn
  • 作者简介:曹慧敏, E-mail: chm98316@163.com;杨贤莉, E-mail: aiwei.ni@163.com **同等贡献
  • 基金资助:
    深圳市基础研究专项(JCYJ20200109150713553);海南省崖州湾种子实验室揭榜挂帅项目(B21HJ0216)

QTL identification and favorable allele mining of cold tolerance at seedling stage by reciprocal introgression and recombinant inbred line populations in rice

CAO Hui-Min1,2(), YANG Xian-Li3(), WANG Li-Zhi3, LI Ping-Ping1, ZHAI Lai-Yuan2, JIANG Shu-Kun3, ZHENG Tian-Qing2, QIU Xian-Jin1(), XU Jian-Long2,4,5()   

  1. 1Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River, Ministry of Agriculture and Rural Affairs (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
    4Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
    5Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China
  • Received:2023-02-16 Accepted:2023-04-17 Published:2023-10-12 Published online:2023-04-24
  • Contact: E-mail: xjqiu216@yangtzeu.edu.cn; E-mail: xujianlong@caas.cn
  • About author:**Contributed equally to this work
  • Supported by:
    Shenzhen Basic Research Special Project(JCYJ20200109150713553);Hainan Yazhou Bay Seed Lab Project(B21HJ0216)

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摘要：

苗期低温冷害常造成水稻生长发育受阻, 影响形态建成最终导致减产。鉴定和挖掘优良的耐冷基因, 选育耐冷水稻品种, 是减少冷害造成水稻产量损失的有效措施。本研究以籼稻明恢63和粳稻02428为亲本构建的双向导入系及重组自交系群体为研究材料, 通过人工气候室进行苗期耐冷性鉴定, 考查枯萎度和冷害恢复生长后的存活率, 结合重测序构建的Bin基因型数据, 进行苗期耐冷性QTL定位, 3个群体在1号、4号、5号、7号和12号染色体上共检测到13个与水稻苗期耐冷性相关的QTL, 解释0.36%~13.63%的表型变异。未定位到不同遗传背景下稳定表达的QTL, 但有5个同时影响枯萎度和存活率的QTL被检出, 分别位于1号、5号、7号和12号染色体, 其中位于1号染色体12,732,139~13,202,097 bp和14,445,778~14,585,009 bp及5号染色体14,658,891~15,684,510 bp的3个QTL的LOD值都高于25, 被认为是可靠的主效QTL。结合基因注释、表达谱数据和3K种质资源的苗期耐冷表型数据分析, 推测位于5号染色体区间内影响枯萎度和存活率的基因很可能是已克隆的耐冷基因OsWKRY45, 而1号染色体2个区间的2个基因是新基因位点, 其候选基因分别是LOC_Os01g25540和LOC_Os01g25560。单倍型分析结果表明, LOC_Os01g25540的Hap2、Hap4和Hap9, LOC_Os01g25560的Hap1、Hap8和Hap10为有利单倍型。研究结果将为水稻品种耐冷分子改良提供宝贵的耐冷资源和有利基因。

关键词: 水稻, 苗期耐冷, 枯萎度, QTL定位, 单倍型

Abstract:

Cold damage often hinders rice growth, affects its morphogenesis and leads finally to serious yield loss. Identifying favorable genes tolerant to cold, and breeding elite rice varieties with cold tolerance is an effective way to solve this problem. In this study, two sets of reciprocal introgression lines and a set of recombinant inbred line derived from xian variety Minghui 63 and geng variety 02428 were evaluated for cold tolerance in climate chamber using cold tolerance-related traits such as wilting degree and survival rate after recovered growth. Combined with the available Bin genotype data generated by previous re-sequencing, 13 QTLs for cold tolerance at seedling stage were identified on chromosomes 1, 4, 5, 7, and 12, which explained 0.36% to 13.63% of phenotypic variation. No QTL was stably detected in different genetic backgrounds, whereas five QTLs were simultaneously detected for both wilting degree and survival rate on chromosomes 1, 5, 7, and 12. Among them, QTLs in the regions of 12,732,139-13,202,097 bp and 14,445,778-14,585,009 bp on chromosome 1, and 14,658,891-15,684,510 bp on chromosome 5 had high LOD values above 25 and were considered as reliable main-effect QTLs. Combined with gene annotation, gene expression profile and phenotyping data of cold tolerance of 3K germplasms, the previously cloned gene OsWKRY45 for cold tolerance was regarded as the responsible gene for the QTL in the region of 14,658,891-15,684,510 bp on chromosome 5, while the two candidate genes, LOC_Os01g25540 and LOC_Os01g25560 in the two regions on chromosome 1, were the new candidate genes for both wilting degree and survival rate. Haplotype analysis indicated that Hap2, Hap4, and Hap9 of LOC_Os01g25540 and Hap1, Hap8, and Hap10 of LOC_Os01g25560 were favorable haplotypes for cold tolerance. The results provide the novel germplasms and favorable genes for molecular improvement of cold tolerance in rice.

Key words: rice, cold tolerance at seedling stage, wilting degree, QTL mapping, haplotype

图1

双向导入系和重组自交系群体的明恢63基因组成成分的频数分布"

表1

亲本、双向导入系和重组自交系群体苗期耐冷表现"

性状
Trait		 明恢63
MH63		 02428 明恢63背景导入系 MH63-ILs 02428背景导入系 02428-ILs 重组自交系 RIL
平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range		 平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range		 平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range
枯萎度
Wilting degree		 8.00 1.00** 8.40±
1.60		 10.07 -3.17 1.00-
9.00		 6.15±
2.91		 -1.30 -0.48 1.00-
9.00		 8.20±
1.80		 6.78 -2.65 1.00-
9.00
存活率
Survival rate (%)		 15.69 81.90** 6.00±
17.00		 12.63 3.53 0-
100.00		 35.00±
36.00		 -1.19 0.58 0-
100.00		 8.00±
20.00		 7.91 2.87 0-
100.00

图2

明恢63和02428衍生群体的苗期耐冷分布"

表2

明恢63和02428衍生群体定位到的苗期耐冷QTL"

群体
Population		 性状
Trait		 染色体
Chr.		 QTL 区间
Interval (bp)		 LOD 加性效应
A		 贡献率
PVE (%)
明恢63背景导入系
MH63-ILs		 枯萎度WD 5 qWD5 14,658,891-15,684,510 28.72 -1.65 8.17
存活率SR 5 qSR5 14,658,891-15,684,510 29.43 0.18 5.86
12 qSR12.1 24,001,167-24,472,105 3.95 0.20 3.28
02428背景导入系
02428-ILs		 枯萎度WD 4 qWD4 1,048,077-1,157,529 7.20 1.15 12.92
12 qWD12 26,529,940-26,660,385 3.03 -0.67 5.20
存活率SR 4 qSR4 764,097-963,403 7.42 −0.15 13.63
12 qSR12.2 26,529,940-26,660,385 2.73 0.08 4.75
重组自交系
RIL		 枯萎度WD 1 qWD1.1 12,732,139-13,202,097 44.95 1.57 9.58
1 qWD1.2 14,445,778-14,585,009 31.63 -1.25 5.91
7 qWD7 16,793,414-17,068,785 2.64 -0.28 0.36
存活率SR 1 qSR1.1 12,732,139-13,202,097 49.88 -0.19 10.67
1 qSR1.2 14,445,778-14,585,009 36.09 0.15 6.71
7 qSR7 16,793,414-17,068,785 3.08 0.03 0.40

图3

明恢63和02428衍生群体定位到的水稻苗期耐冷QTL在染色体上的分布 WD: 枯萎度; SR: 存活率。"

图4

2个候选基因的单倍型分析图 A、D: 2个耐冷性状不同单倍型间的表型差异, 不同字母代表不同单倍型之间表型在P < 0.01水平差异显著; B、E: 不同亚群在不同单倍型内的频率分布; C: 低温和常温条件下空育131苗期叶片LOC_os01g22540的表达量(数据来源于Yu等[18]的报道); F: 低温和常温条件下日本晴苗期根部LOC_os01g22560的表达量(数据来源于Yu等[18]的报道); **和***分别代表表达量在P < 0.01和P < 0.001水平差异显著。"

附表1

两个候选基因的单倍型信息"

候选基因
Candidate gene		 单倍型编号
Hap ID		 单倍型
Haplotype (5′-3′)		 种质资源数目 No. of accessions
籼稻
xian		 粳稻
geng		 Aus Bas 中间型
Admix
LOC_Os01g25540 Hap1 GCTATTGGACCAGAACCCGTAGGAGGCCACCTGCAGCCACTGCAGCGAAGCGAG 110 4 37 9 4
Hap2 GAGACTGGATCGGATCCCGTGGGGGGCTGCCTATAGCCACTGTGGCAAAGCGGA 1 138 0 1 3
Hap3 TCGATTAGACCAGAACTAGTAGGAGGCCACCTGCAGCCACTGTGGCGAAGCGGA 123 0 0 0 2
Hap4 TCGATTAGGCCAGAACCAGTAGGAGGTCACCTGCAGCCACTGTGGAGAAGCGGA 96 0 0 0 1
Hap5 GAGGCCGGATTAAACCCCGTGGAGGGCCACCTATAGCCACTGTGTAGAAGCGGG 37 0 40 1 4
Hap6 TCGATTGAACCAGAACCCGTAGGGGGCCACTTGCAGCCACAGTGGAGAAACGGA 57 0 0 0 1
Hap7 GAGGCTGGATTAGACCCCATGGGGGGTCATCTATGGCTACTGTAGCGAAGCGGG 49 0 0 0 2
Hap8 GCTATTGGACCAGAACCCGTAGGAGGCCACCTGCAGCCACTGTAGCGAAGCGAG 42 0 0 0 0
Hap9 GAGACTGGATCGGATCCCGTGGGGGACTGCCTATAGCCACTGTGGCAAAGCGGA 0 28 0 0 2
LOC_Os01g25560 Hap1 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCCAAG 5 344 0 8 14
Hap2 TCCGGTGCAGAGCTGGGAGCGTTAGCGTTCCTATCAGG 155 0 0 0 3
Hap3 TTCGGCGCAGAGCTGGGGGCGCTGGCGGCCCTATCAGG 136 3 12 0 3
Hap4 TCAGGCGCAGAGCTGGGAGCGTTAGCGGCCCTATCAGG 109 0 0 0 0
Hap5 TCCGGCGCAGAGCTGGAAGCGTTAGCGGCCCTATCAGG 89 0 0 0 0
Hap6 TCCGGCGCAGAGCTAAGAGCGTTAACGGCCCGATCAGA 29 0 52 0 5
Hap7 TCCGACGCAGAGCTGGGAGCGTTAGCCGCCCTATCAGG 41 0 33 7 2
Hap8 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCCMAG 1 76 0 0 2
Hap9 TCCGGCGCAGAGCTGAGATCGTTAGCGGCTCTATTAGG 60 0 1 0 1
Hap10 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCC-AG 1 37 0 3 6
Hap11 TTCGGCGCAGAGCTGGGGGCGCTGGCGGCCCTATC-GG 31 0 3 0 0
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