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作物学报 ›› 2022, Vol. 48 ›› Issue (9): 2255-2264.doi: 10.3724/SP.J.1006.2022.12033

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

对水稻种子耐储性QTL的研究

黄祎雯1,2(), 孙滨2(), 程灿2, 牛付安2, 周继华2, 张安鹏2, 涂荣剑2, 李瑶2,3, 姚瑶1,2, 代雨婷1,2, 谢开珍2,3, 陈小荣1, 曹黎明2,*(), 储黄伟2,*()   

  1. 1.江西农业大学农学院, 江西南昌 330045
    2.上海市农业科学院作物育种栽培研究所, 上海 201403
    3.上海海洋大学水产与生命学院, 上海 201306
  • 收稿日期:2021-05-06 接受日期:2022-01-05 出版日期:2022-09-12 网络出版日期:2022-02-14
  • 通讯作者: 曹黎明,储黄伟
  • 作者简介:黄祎雯, E-mail: 1564903141@qq.com;
    孙滨, E-mail: sunbin@saas.sh.cn第一联系人：

    ** 同等贡献

QTL mapping of seed storage tolerance in rice (Oryza sativa L.)

HUANG Yi-Wen1,2(), SUN Bin2(), CHENG Can2, NIU Fu-An2, ZHOU Ji-Hua2, ZHANG An-Peng2, TU Rong-Jian2, LI Yao2,3, YAO Yao1,2, DAI Yu-Ting1,2, XIE Kai-Zhen2,3, CHEN Xiao-Rong1, CAO Li-Ming2,*(), CHU Huang-Wei2,*()   

  1. 1. School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
    2. Institute of crop breeding and cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
    3. College of Fisheries and life, Shanghai Ocean University, Shanghai 201306, China
  • Received:2021-05-06 Accepted:2022-01-05 Published:2022-09-12 Published online:2022-02-14
  • Contact: CAO Li-Ming,CHU Huang-Wei
  • About author:First author contact:

    ** Contributed equally to this work

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摘要：

稻谷的耐储性在种子生产保存和粮食储备中具有重要的意义。本研究以人工陈化的方法对15个三系杂交稻恢复系品种进行筛选, 获得了繁11、繁12、繁31、繁32和繁38五个耐储性较好的品种。选择繁38与粳型恢复系繁26为亲本杂交获得F1代, 构建了包含154个株系的双单倍体(double haploid, DH)群体。以2b-RAD简化基因组测序技术对亲本和群体中每个株系进行测序, 并构建SNP标记遗传图谱。分析水稻在人工陈化10 d和15 d时与耐储藏相关的QTL。共检测到了6个与稻谷耐储性相关的QTL位点, 分布于3号、5号、6号、11号和12号染色体上, LOD值介于3.4509~6.8036之间, 可解释6.1575%~12.9979%的表型变异, 加性效应在-6.7586%到6.1235%范围内。其中qSI-12位点在陈化10 d和陈化15 d两个条件下均能检测到。qSI-5a和qSI-6这2个位点只在陈化10 d时检测到, 而qSI-3、qSI-5b和qSI-11这3个位点只在陈化15 d时检测到。此外, 还检测到32对上位性互作位点。这些结果丰富了耐储性品种育种的遗传资源, 为进一步精细定位耐储性相关的QTL奠定了基础。

关键词: 水稻, 耐储藏, 人工陈化, QTL分析, DH群体

Abstract:

Rice seed storability is great significance in seed production and grain storage. In this study, 15 three-line hybrid rice restorer varieties were screened by artificial aging method, and 5 varieties with good storage tolerance (namely Fan 11, Fan 12, Fan 31, Fan 32, and Fan 38) were obtained. A Double Haploid (DH) population including 154 lines was constructed using F1 derived from the crossing between storage tolerance variety, Fan 38, and japonica restorer line, Fan 26. The parents and DH lines were sequenced using 2bB-RAD Reduced-Representation Genome Sequencing, and a genetic linkage map of SNP marker was constructed. QTLs related to storage tolerance after 10 days and 15 days artificial aging for were analyzed, respectively. A total of 6 QTL loci related to rice storage tolerance were detected on chromosomes 3, 5, 6, 11, and 12, with LOD values ranging from 3.4509 to 6.8036, explaining phenotypic variation of 6.1575%-12.9979%, and the additive effect ranged from -6.7586% to 6.1235%. The qSI-12 locus could be detected under both 10-day and 15-day aging conditions. qSI-5a and qSI-6 were detected only after 10 days of artificial aging, while qSI-3, qSI-5b, and qSI-11 were detected only after 15 days of artificial aging. In addition, 32 pairs of epistatic interaction sites were detected. These results enriched the genetic resources for the breeding of storage tolerance varieties, and laid a foundation for further fine mapping of QTLs related to storage tolerance.

Key words: rice, storage, artificial aging, QTLs analysis, double haploid population

表1

耐储藏水稻品种的筛选"

品种
Variety		 发芽率(%, 平均值±标准差) Germination rate (%, mean±SD) 耐储藏指数
Storability index (%)		 籼型指数
Indica index Fi
对照 Control 陈化15 d Aged for 15 days
繁1 Fan 1 91.67±2.36 13.33±4.71 14.55 0.12
繁3 Fan 3 92.22±1.92 23.33±3.33 25.30 0.18
繁6 Fan 6 90.00±3.33 2.22±1.92 2.47 0.15
繁9 Fan 9 90.00±8.81 0.00±0.00 0 0.15
繁10 Fan 10 93.33±4.71 0.00±0.00 0 0.15
繁11 Fan 11 83.33±6.67 46.67±6.67 56.00 0.41
繁12 Fan 12 90.00±5.77 63.33±0.00 70.37 0.18
繁14 Fan 14 87.78±5.09 0.00±0.00 0 0.18
繁16 Fan 16 96.67±0.00 30.00±3.33 31.03 0.21
繁24 Fan 24 95.56±5.09 0.00±0.00 0 0.21
繁26 Fan26 96.67±3.33 4.44±3.85 4.60 0.21
繁29 Fan 29 97.78±1.92 0.00±0.00 0.00 0.24
繁31 Fan 31 91.11±3.85 48.33±7.07 53.05 0.85
繁32 Fan 32 93.33±5.77 58.89±5.09 63.10 0.91
繁38 Fan 38 97.78±3.84 72.22±8.39 73.86 0.88

图1

不同人工陈化时间水稻亲本的发芽情况(a)和发芽率(b)"

图2

人工陈化10 d (a)和15 d (b) DH群体耐储藏指数分布情况"

表2

人工陈化10 d和15 d亲本及DH群体的耐储藏"

陈化天数
Artificial aging time		 亲本Parents 单双倍体群体DH population
繁26
Fan 26		 繁38
Fan 38		 平均值±标准差Mean±SD 区间
Range		 偏斜
Skewness		 峰度
Kurtosis
10 d 43.10 79.55 58.16±21.08 7.09-99.26 -0.20 -0.32
15 d 4.60 73.86 14.20±14.84 0-65.19 1.47 1.69

表3

人工陈化条件下水稻种子耐储藏性状QTL定位"

性状
Trait		 位点
Locus		 位置
Position (cM)		 标记区间
Marker range		 范围
Range (bp)		 LOD值
LOD value		 贡献率
PVE (%)		 加性效应
Additive effect (%)
0-10 d qSI-5a 40 Chr. 5: 56-59 7,208,572-7,851,620 4.5867 8.9836 -6.7586
qSI-6 59 Chr. 6: 143-200 7,984,061-9,393,696 3.7526 7.2240 6.1235
qSI-12 109 Chr. 12: 338-357 27,172,724-27,529,089 4.5403 8.8263 -6.7220
0-15 d qSI-3 23 Chr. 3: 191-195 9,836,591-9,908,839 6.8036 12.9979 -6.6611
qSI-5b 54 Chr. 5: 21-36 1,425,225-6,314,136 3.4682 7.7014 -4.3016
qSI-11 31 Chr. 11: 63-65 3,179,591-3,286,377 6.2939 11.7685 5.5123
qSI-12 109 Chr. 12: 338-357 27,172,724-27,529,089 3.4509 6.1575 -3.8607

附表2

水稻12条染色体遗传标记的分布"

染色体 连锁群 标记个数 遗传长度 平均区间 最大区间长度 标记之间的平均物理距离
Chromosome Linkage group No. of markers Genetic length (cM) Average interval (cM) Max. interval length (cM) Average physical distance between markers (kb)
1 1-1 9 17.07 1.9 5.99 479.7
1-2 74 100.47 1.36 7.96 381.38
2 2-1 13 15.18 1.17 1.97 921.47
2-2 10 13.26 1.33 3.28 902.32
2-3 16 38.9 2.43 21.69 651.16
3 3 77 125.84 1.63 13.95 472.91
4 4-1 44 70.97 1.61 4.71 571.43
4-2 16 13.94 0.87 1.98 169.8
5 5 53 109.26 2.06 23.08 565.25
6 6-1 4 5.39 1.35 3.41 270.57
6-2 51 106.92 2.1 18.22 567.39
7 7 33 94.59 2.87 15.84 899.93
8 8 66 123.28 1.87 15.55 430.95
9 9 33 80.73 2.45 15.11 697.36
10 10 64 80.48 1.26 10 362.61
11 11 56 112.48 2.01 15.4 518.23
12 12-1 9 6.66 0.74 1.35 244.07
12-2 38 53.44 1.41 8.13 484.94
总计Overal 总计Overal 666 1168.86 1.69 23.08 594.64

图3

人工陈化条件下水稻种子耐储藏性状QTL在DH群体中染色体分布(a)和上位性分析(b) 红色和蓝色虚线分别表示人工陈化10 d和15 d时检测到的上位性效应。"

附表3

人工老化条件下水稻种子耐储藏性状上位性分析"

TraitID TraitName Chromosome1 Position1 LeftMarker1 RightMarker1 Chromosome2 Position2 LeftMarker2 RightMarker2 LOD PVE (%) Add1 Add2 AddbyAdd
1 10d 1 178 ch1-770 ch1-773 4 109 ch4-643 ch4-649 2.5344 2.9461 -0.3359 -0.3593 4.7714
1 10d 1 125 ch1-336 ch1-344 5 97 ch5-385 ch5-388 3.1207 4.8485 -1.9963 1.7157 5.3383
1 10d 4 5 ch4-89 ch4-90 6 63 ch6-263 ch6-289 2.6415 3.022 0.9242 1.6863 5.1041
1 10d 3 24 ch3-191 ch3-195 7 8 ch7-23 ch7-25 2.8394 3.8246 -3.0147 1.7443 -6.2923
1 10d 2 39 ch2-64 ch2-90 7 60 ch7-278 ch7-280 2.6974 12.0232 4.3933 -2.356 9.5701
1 10d 7 9 ch7-25 ch7-36 7 89 ch7-307 ch7-308 2.6536 4.1307 -2.7874 -2.5645 -5.1543
1 10d 10 5 ch10-97 ch10-129 10 42 ch10-567 ch10-573 2.5463 3.1451 -1.1836 1.1202 5.879
1 10d 11 32 ch11-65 ch11-86 11 63 ch11-427 ch11-433 2.5051 3.056 1.9739 0.7077 5.8484
1 10d 10 41 ch10-563 ch10-567 12 105 ch12-325 ch12-334 2.5924 2.9598 -0.0015 1.2774 -5.0737
2 15d 1 42 ch1-159 ch1-161 3 23 ch3-171 ch3-183 3.5395 4.97 5.9472 -2.188 -7.6707
2 15d 2 39 ch2-64 ch2-90 3 23 ch3-171 ch3-183 3.8744 4.1072 -5.6799 -0.9674 6.492
2 15d 3 100 ch3-807 ch3-837 3 105 ch3-843 ch3-864 2.8365 3.4799 1.4227 -0.2099 -10.9405
2 15d 3 1 ch3-7 ch3-10 4 62 ch4-556 ch4-560 3.2662 1.9326 1.7679 -1.934 3.8366
2 15d 1 117 ch1-290 ch1-297 4 97 ch4-596 ch4-598 3.3181 1.9115 -0.3325 -0.1728 3.8793
2 15d 4 35 ch4-469 ch4-475 5 89 ch5-356 ch5-363 2.641 1.4086 0.4091 0.6815 -3.2696
2 15d 3 23 ch3-171 ch3-183 6 3 ch6-25 ch6-26 2.5169 1.3794 0.1209 2.6377 -3.943
2 15d 4 79 ch4-596 ch4-598 6 132 ch6-615 ch6-617 3.2659 2.8512 -1.5125 -1.146 4.521
2 15d 3 23 ch3-171 ch3-183 7 8 ch7-23 ch7-25 3.0178 1.5174 -1.5646 3.1367 -4.459
2 15d 1 1 ch1-13 ch1-43 8 2 ch8-10 ch8-11 3.1271 1.5583 0.0639 0.042 3.5058
2 15d 3 44 ch3-315 ch3-341 8 123 ch8-640 ch8-644 4.0312 2.9516 -3.7635 5.5518 -5.5205
2 15d 2 87 ch2-301 ch2-313 9 61 ch9-298 ch9-306 2.6537 1.3775 5.363 0.5894 6.4891
2 15d 5 50 ch5-169 ch5-187 9 62 ch9-306 ch9-308 2.5355 1.3666 -6.8271 2.2675 -7.3989
2 15d 3 24 ch3-191 ch3-195 9 80 ch9-406 ch9-407 3.5678 5.5949 -11.0377 5.6481 -6.6336
2 15d 3 50 ch3-428 ch3-431 10 6 ch10-132 ch10-135 2.5985 1.859 -4.8706 5.944 -5.3614
2 15d 10 16 ch10-361 ch10-375 10 25 ch10-417 ch10-425 3.2299 2.1018 4.075 -3.7495 -6.864
2 15d 6 133 ch6-615 ch6-617 10 80 ch10-725 ch10-734 3.6547 2.7463 -1.5399 1.8084 -4.0638
2 15d 8 2 ch8-10 ch8-11 11 59 ch11-194 ch11-319 2.9629 1.5471 1.5843 0.9499 3.7992
2 15d 6 65 ch6-289 ch6-533 11 62 ch11-411 ch11-427 3.309 1.86 -2.9826 -0.1096 -3.9808
2 15d 7 36 ch7-243 ch7-247 11 87 ch11-459 ch11-467 3.0592 2.1895 -0.3598 -1.324 -4.0831
2 15d 12 25 ch12-43 ch12-46 12 27 ch12-43 ch12-46 3.5769 8.1352 -6.8067 8.0638 -4.4508
2 15d 4 3 ch4-66 ch4-72 12 31 ch12-43 ch12-46 2.7726 2.8824 0.0306 -0.4339 -4.8661
2 15d 3 105 ch3-843 ch3-864 12 72 ch12-232 ch12-235 2.9506 1.6021 0.5047 0.7086 -3.5864
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