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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (9): 2255-2264.doi: 10.3724/SP.J.1006.2022.12033

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2022-09-12 Published:2022-02-14
  • Contact: CAO Li-Ming,CHU Huang-Wei E-mail:1564903141@qq.com;sunbin@saas.sh.cn;caoliming@saas.sh.cn;chuhuangwei@saas.sh.cn
  • About author:First author contact:

    ** Contributed equally to this work

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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

Table 1

Selection of storage tolerant in rice varieties"

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

Fig. 1

Germination status (a) and rate (b) of rice parents with different artificial aging time"

Fig. 2

Distribution of storage tolerance index of rice DH population at artificial aging time of 10 days (a) and 15 days (b)"

Table 2

Storage tolerance index of parents and DH population after 10 days and 15 days artificial aging"

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

Table 3

QTL mapping for storage tolerance of rice seeds under artificial aging"

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

Table S2

Distribution of genetic markers across the 12 chromosomes in rice"

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

Fig. 3

Chromosome distribution of QTLs for storage tolerance of rice seeds in DH population under artificial aging (a) and Epistasis analysis (b) The red and blue dashed lines indicate epistatic effects detected at 10- and 15-days artificial aging, respectively."

Table S3

Epistatic analysis for storage tolerance of rice seeds under artificial aging"

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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