中国农业科学 ›› 2021, Vol. 54 ›› Issue (24): 5163-5176.doi: 10.3864/j.issn.0578-1752.2021.24.001
张亚东(),梁文化,赫磊,赵春芳,朱镇,陈涛,赵庆勇,赵凌,姚姝,周丽慧,路凯,王才林
收稿日期:
2021-06-07
接受日期:
2021-08-03
出版日期:
2021-12-16
发布日期:
2021-12-28
通讯作者:
王才林
作者简介:
张亚东,E-mail: 基金资助:
ZHANG YaDong(),LIANG WenHua,HE Lei,ZHAO ChunFang,ZHU Zhen,CHEN Tao,ZHAO QingYong,ZHAO Ling,YAO Shu,ZHOU LiHui,LU Kai,WANG CaiLin
Received:
2021-06-07
Accepted:
2021-08-03
Online:
2021-12-16
Published:
2021-12-28
Contact:
CaiLin WANG
摘要:
【目的】水稻粒型是与产量直接相关的重要农艺性状,影响稻米的外观品质和商品价值。挖掘新的水稻粒型相关基因,对揭示水稻粒型调控的遗传机理研究有重要意义,同时可为水稻粒型分子育种提供新的基因资源。【方法】以极端粒型差异的粳稻TD70和籼稻Kasalath,以及杂交构建的186个家系的重组自交系群体为研究材料,利用高通量测序技术对亲本和RIL株系进行深度测序。统计186个RIL基因型数据,利用滑动窗法(SNP/InDel数目为15),将窗口内SNP/InDel信息转换成窗口的基因型,预测染色体上的重组断点构建RIL群体的BinMap遗传图谱,结合2年的粒长、粒宽、粒厚和千粒重的表型数据,运用QTL IciMapping软件,采用复合区间作图法对RIL群体的4个性状进行QTL定位。【结果】构建了一张包含12 328个Bin标记的高密度遗传图谱,该图谱各染色体Bin标记数为763—1 367个,标记间平均物理距离为30.26 kb。粒长、粒宽、粒厚和千粒重4个性状在RIL群体中呈近正态连续分布,且2年间的变化趋势相似,符合QTL作图要求。2018年对粒长、粒宽、粒厚及千粒重进行QTL分析,共检测到40个粒型QTL,其中,粒长12个,粒宽9个,粒厚8个,千粒重11个,2019年对粒长、粒宽、粒厚及千粒重进行QTL分析,检测到56个籽粒相关的QTL,粒长15个,粒宽11个,粒厚13个,千粒重17个。分析定位到的96个粒型QTL位点,连续2年都能检测到的QTL位点有11个,其中7个为已克隆的粒型基因位点,4个为未知的新位点,分别分布于第1、3、4、5染色体上,分别为粒长qGL-1-2和qGL5-2、粒厚qGT-3-2、粒宽qGW-4-1。【结论】构建了一张包含12 328个Bin标记的分子遗传连锁图谱,解析大粒粳稻资源的粒型基因,获得了qGW-4-1、qGL5-2、qGT-3-2、qGL-1-2等4个新的粒型QTL,可用于后续粒型调控基因的精细定位及克隆研究。
张亚东,梁文化,赫磊,赵春芳,朱镇,陈涛,赵庆勇,赵凌,姚姝,周丽慧,路凯,王才林. 水稻RIL群体高密度遗传图谱构建及粒型QTL定位[J]. 中国农业科学, 2021, 54(24): 5163-5176.
ZHANG YaDong,LIANG WenHua,HE Lei,ZHAO ChunFang,ZHU Zhen,CHEN Tao,ZHAO QingYong,ZHAO Ling,YAO Shu,ZHOU LiHui,LU Kai,WANG CaiLin. Construction of High-Density Genetic Map and QTL Analysis of Grain Shape in Rice RIL Population[J]. Scientia Agricultura Sinica, 2021, 54(24): 5163-5176.
表1
亲本与RIL群体2年间粒型的表型变异"
性状 Trait | 年份 Year | 亲本 Parents | 重组自交系 RIL populations | |||
---|---|---|---|---|---|---|
TD70 | Kasalath | 平均值 Average | 变异范围 Range | 变异系数 CV (%) | ||
粒长 GL (mm) | 2018 | 13.40 | 8.04 | 9.72 | 7.77—13.00 | 12.72 |
2019 | 13.29 | 8.07 | 9.58 | 7.42—12.74 | 12.57 | |
粒宽 GW (mm) | 2018 | 4.42 | 2.48 | 3.12 | 2.37—4.34 | 11.52 |
2019 | 4.29 | 2.48 | 3.11 | 2.31—4.42 | 11.88 | |
粒厚 GT (mm) | 2018 | 2.99 | 1.84 | 2.10 | 1.71—2.63 | 7.35 |
2019 | 2.93 | 1.90 | 2.17 | 1.79—2.78 | 8.12 | |
千粒重 TGW (g) | 2018 | 64.95 | 17.40 | 30.60 | 17.95—55.40 | 22.58 |
2019 | 66.52 | 17.83 | 27.99 | 14.77—49.75 | 22.68 |
表2
Bin图谱信息表"
染色体 Chromosome | Bin个数 Bin number | 遗传距离 Genetic distance (cM) | 标记平均距离 Mean distance between markers (cM) |
---|---|---|---|
1 | 1367 | 2173.32 | 1.589846379 |
2 | 991 | 1290.30 | 1.302018163 |
3 | 948 | 1158.52 | 1.222067511 |
4 | 1177 | 2400.93 | 2.039872557 |
5 | 954 | 1522.71 | 1.596132075 |
6 | 1103 | 1849.13 | 1.676455122 |
7 | 1032 | 2198.84 | 2.130658915 |
8 | 1045 | 2055.74 | 1.967215311 |
9 | 788 | 1453.83 | 1.844961929 |
10 | 763 | 1006.01 | 1.318492792 |
11 | 1098 | 1938.07 | 1.765091075 |
12 | 1062 | 2248.04 | 2.116798493 |
表3
粒型性状QTL分析"
性状与位点 Trait and loc | 染色体 Chr. | 标记区间 Marker interval | 关联基因 Cloned gene | LOD值 LOD score | 贡献率PVE (%) | 加性效应 Additive | |||
---|---|---|---|---|---|---|---|---|---|
2018 | 2019 | 2018 | 2019 | 2018 | 2019 | ||||
粒长 GL | |||||||||
qGL-1-1 | 1 | RBN0626—RBN0627 | 3.32 | 1.41 | -0.14 | ||||
qGL-1-2* | 1 | RBN0752—RBN0746 | 3.60 | 3.15 | -0.29 | ||||
qGL-2-2 | 2 | RBN2285—RBN2286 | TGW2 | 7.47 | 8.27 | 4.26 | 3.69 | -0.22 | -0.23 |
qGL-2-1 | 2 | RBN1612—RBN1613 | 4.47 | 2.00 | -0.16 | ||||
qGL-2-3 | 2 | RBN2346—RBN2347 | 3.31 | 1.50 | 0.62 | ||||
qGL-3-1 | 3 | RBN2661—RBN2665 | 10.97 | 6.66 | 0.87 | ||||
qGL-3-2 | 3 | RBN2808—RBN2809 | GS3 | 27.88 | 27.05 | 20.94 | 15.44 | -0.48 | -0.46 |
qGL-3-3 | 3 | RBN2901—RBN2900 | 11.36 | 6.77 | -0.29 | ||||
qGL-3-4 | 3 | RBN2915—RBN2916 | 12.62 | 5.79 | -0.29 | ||||
qGL-3-5 | 3 | RBN3000—RBN2997 | qGL3/GL3.1 | 27.50 | 22.49 | 21.26 | 12.55 | -0.52 | -0.44 |
qGL-4 | 4 | RBN4252—RBN4253 | XIAO | 10.85 | 8.37 | 6.66 | 3.86 | -0.27 | -0.22 |
qGL-5-1 | 5 | RBN4645—RBN4646 | 7.43 | 3.36 | 0.21 | ||||
qGL-5-2** | 5 | RBN5163—RBN5167 | 5.81 | 4.31 | 5.13 | 4.55 | -0.29 | -0.24 | |
性状与位点 Trait and loc | 染色体 Chr. | 标记区间 Marker interval | 关联基因 Cloned gene | LOD值 LOD score | 贡献率PVE (%) | 加性效应 Additive | |||
2018 | 2019 | 2018 | 2019 | 2018 | 2019 | ||||
qGL-7-1 | 7 | RBN6899—RBN6900 | 3.22 | 1.48 | 0.56 | ||||
qGL-7-2 | 7 | RBN7397—RBN7393 | 15.55 | 7.44 | 0.31 | ||||
qGL-7-3 | 7 | RBN7400—RBN7402 | GL7/GW7 | 10.13 | 33.76 | 5.99 | 21.17 | 0.26 | 0.53 |
qGL-8 | 8 | RBN8430—RBN8434 | GW8 | 7.30 | 4.13 | -0.25 | |||
qGL-9 | 9 | RBN8628—RBN8629 | 2.58 | 1.02 | 0.39 | ||||
qGL-11 | 11 | RBN11026—RBN11027 | 3.99 | 2.21 | -0.16 | ||||
qGL-12-1 | 12 | RBN11481—RBN11482 | LARGE2 | 5.36 | 3.00 | 0.18 | |||
qGL-12-2 | 12 | RBN11605—RBN11608 | 4.99 | 2.14 | 0.17 | ||||
粒宽 GW | |||||||||
qGW-2-1 | 2 | RBN1385—RBN1387 | 7.16 | 4.55 | -0.08 | ||||
qGW-2-2 | 2 | RBN1564—RBN1566 | GW2 | 35.15 | 32.03 | 28.82 | 30.07 | -0.20 | -0.21 |
qGW-2-3 | 2 | RBN2138—RBN2136 | 8.47 | 5.61 | -0.09 | ||||
qGW-2-4 | 2 | RBN2203—RBN2204 | GS2 | 3.05 | 1.61 | -0.05 | |||
qGW-4-1** | 4 | RBN3403—RBN3404 | 5.17 | 3.22 | 3.05 | 3.65 | 0.13 | -0.38 | |
qGW-4-2 | 4 | RBN4252—RBN4253 | XIAO | 4.40 | 2.50 | 0.06 | |||
qGW-4-3 | 4 | RBN4420—RBN4421 | 12.66 | 7.73 | -0.10 | ||||
qGW-4-4 | 4 | RBN4427—RBN4428 | 5.45 | 3.48 | -0.07 | ||||
qGW-5 | 5 | RBN4641—RBN4642 | GW5 | 32.44 | 22.82 | 25.59 | 18.31 | -0.18 | -0.16 |
qGW-7-1 | 7 | RBN7188—RBN7189 | GLW7 | 7.20 | 4.11 | -0.07 | |||
qGW-7-2 | 7 | RBN7481—RBN7482 | 5.03 | 2.78 | -0.09 | ||||
qGW-8-1 | 8 | RBN7840—RBN7842 | 3.51 | 2.71 | -0.41 | ||||
qGW-8-2 | 8 | RBN8134—RBN8135 | 3.98 | 2.54 | -0.06 | ||||
qGW-9-1 | 9 | RBN8981—RBN8988 | 4.87 | 3.07 | 0.06 | ||||
qGW-10-1 | 10 | RBN9497—RBN9501 | 2.53 | 1.60 | -0.23 | ||||
qGW-11-1 | 11 | RBN10406—RBN10407 | SRS5/TID1/OsTubA2 | 3.84 | 2.80 | -0.19 | |||
qGW-11-2 | 11 | RBN10496—RBN10497 | 3.40 | 2.21 | 0.06 | ||||
粒厚 GT | |||||||||
qGT-1 | 1 | RBN0651—RBN0652 | 8.59 | 6.82 | -0.05 | ||||
qGT-2-1 | 2 | RBN1564—RBN1566 | GW2 | 31.44 | 33.33 | -0.09 | |||
qGT-2-2 | 2 | RBN1569—RBN1573 | 11.80 | 9.67 | -0.05 | ||||
qGT-2-3 | 2 | RBN1609—RBN1610 | 17.82 | 16.27 | -0.06 | ||||
qGT-3-1 | 3 | RBN2565—RBN2566 | 5.28 | 4.06 | -0.03 | ||||
qGT-3-2* | 3 | RBN2710—RBN2711 | 6.32 | 5.01 | -0.04 | ||||
qGT-3-3 | 3 | RBN2782—RBN2783 | 4.43 | 3.36 | 0.03 | ||||
qGT-3-4 | 3 | RBN2901—RBN2900 | 5.78 | 4.33 | -0.04 | ||||
qGT-3-5 | 3 | RBN2987—RBN2986 | 10.68 | 8.76 | -0.05 | ||||
qGT-4-1 | 4 | RBN3413—RBN3414 | 5.28 | 4.14 | 0.03 | ||||
qGT-4-2 | 4 | RBN3548—RBN3549 | 3.56 | 2.67 | 0.03 | ||||
qGT-5-1 | 5 | RBN4661—RBN4663 | 9.81 | 7.77 | -0.04 | ||||
性状与位点 Trait and loc | 染色体 Chr. | 标记区间 Marker interval | 关联基因 Cloned gene | LOD值 LOD score | 贡献率PVE (%) | 加性效应 Additive | |||
2018 | 2019 | 2018 | 2019 | 2018 | 2019 | ||||
qGT-5-2 | 5 | RBN4668—RBN4669 | 8.16 | 6.66 | -0.04 | ||||
qGT-7 | 7 | RBN7494—RBN7495 | 7.86 | 6.04 | 0.04 | ||||
qGT-8 | 8 | RBN7851—RBN7852 | 3.21 | 2.51 | -0.02 | ||||
qGT-10-1 | 10 | RBN10072—RBN10074 | 5.68 | 4.49 | -0.03 | ||||
qGT-10-2 | 10 | RBN10129—RBN10126 | 2.88 | 2.11 | -0.02 | ||||
qGT-11 | 11 | RBN10949—RBN10950 | 3.43 | 2.73 | 0.03 | ||||
qGT-12-1 | 12 | RBN11790—RBN11791 | 6.85 | 5.44 | -0.05 | ||||
qGT-12-2 | 12 | RBN11823—RBN11824 | 4.22 | 3.18 | 0.05 | ||||
qGT-12-3 | 12 | RBN11866—RBN11879 | 4.67 | 3.60 | 0.03 | ||||
千粒重 TGW | |||||||||
qTGW-1-1 | 1 | RBN0261—RBN0262 | 3.99 | 2.48 | -1.03 | ||||
qTGW-1-2* | 1 | RBN0752—RBN0746 | 22.24 | 11.34 | -2.38 | ||||
qTGW-1-3 | 1 | RBN0767—RBN0766 | 10.25 | 4.31 | 1.46 | ||||
qTGW-2-1 | 2 | RBN1564—RBN1566 | GW2 | 19.35 | 14.68 | -2.55 | |||
qTGW-2-2 | 2 | RBN1630—RBN1631 | 27.16 | 14.59 | -2.56 | ||||
qTGW-2-3 | 2 | RBN1917—RBN1918 | 7.12 | 2.85 | 1.21 | ||||
qTGW-2-4 | 2 | RBN2043—RBN2044 | 7.52 | 3.31 | -1.32 | ||||
qTGW-2-5 | 2 | RBN2121—RBN2120 | 4.43 | 3.42 | -1.28 | ||||
qTGW-3-1 | 3 | RBN2539—RBN2536 | 8.19 | 3.31 | -1.55 | ||||
qTGW-3-2* | 3 | RBN2710—RBN2711 | 8.56 | 6.07 | -1.69 | ||||
qTGW-3-3 | 3 | RBN2827—RBN2828 | 9.97 | 4.24 | -1.42 | ||||
qTGW-3-4 | 3 | RBN2901—RBN2900 | 33.78 | 31.19 | -3.91 | ||||
qTGW-3-5 | 3 | RBN3000—RBN2997 | qGL3/GL3.1 | 23.36 | 12.38 | -2.50 | |||
qTGW-4-1 | 4 | RBN3699—RBN3697 | 3.30 | 2.03 | 0.96 | ||||
qTGW-4-2 | 4 | RBN4427—RBN4428 | 5.81 | 2.31 | -1.00 | ||||
qTGW-5-1 | 5 | RBN4536—RBN4537 | OsMKP1/GSN1 | 3.64 | 2.26 | 0.98 | |||
qTGW-5-2 | 5 | RBN4618—RBN4620 | GS5 | 9.63 | 6.55 | -1.65 | |||
qTGW-5-3 | 5 | RBN4702—RBN4701 | GSK2 | 7.36 | 2.97 | -1.13 | |||
qTGW-6-1 | 6 | RBN5529—RBN5530 | 8.91 | 4.03 | -1.37 | ||||
qTGW-6-2 | 6 | RBN5538—RBN5539 | TGW6 | 11.92 | 5.15 | 1.47 | |||
qTGW-7-1 | 7 | RBN7400—RBN7402 | GL7/GW7 | 6.37 | 4.13 | 1.32 | |||
qTGW-7-2 | 7 | RBN7516—RBN7517 | 9.62 | 4.03 | -1.30 | ||||
qTGW-10 | 10 | RBN10129—RBN10126 | 3.41 | 2.12 | -0.97 | ||||
qTGW-11-1 | 11 | RBN10406—RBN10407 | SRS5/TID1/OsTubA2 | 2.71 | 1.17 | -1.70 | |||
qTGW-11-2 | 11 | RBN10523—RBN10524 | 5.27 | 3.73 | -1.67 | ||||
qTGW-11-3 | 11 | RBN11260—RBN11261 | 4.38 | 2.14 | -1.01 | ||||
qTGW-12-1 | 12 | RBN11790—RBN11791 | 10.85 | 4.63 | -1.91 | ||||
qTGW-12-2 | 12 | RBN11948—RBN11949 | 5.54 | 2.19 | 1.10 |
[1] | 徐正进, 陈温福, 马殿荣, 吕英娜, 周淑清, 刘丽霞. 稻谷粒形与稻米主要品质性状的关系. 作物学报, 2004, 30(9):894-900. |
XU Z J, CHEN W F, MA D R, LÜ Y N, ZHOU S Q, LIU L X. Correlations between rice grain shapes and main qualitative characteristics. Acta Agronomica Sinica, 2004, 30(9):894-900. (in Chinese) | |
[2] | 高志强, 占小登, 梁永书, 程式华, 曹立勇. 水稻粒形性状的遗传及相关基因定位与克隆研究进展. 遗传, 2011, 33(4):314-321. |
GAO Z Q, ZHAN X D, LIANG Y S, CHENG S H, CAO L Y. Progress on genetics of rice grain shape trait and its related gene mapping and cloning. Hereditas, 2011, 33(4):314-321. (in Chinese) | |
[3] | HARBERD N P. Shaping taste: The molecular discovery of rice genes improving grain size, shape and quality. Journal of Genetics & Genomics, 2015, 42(11):597-599. |
[4] |
彭强, 李佳丽, 张大双, 姜雪, 邓茹月, 吴健强, 朱速松. 不同环境基于高密度遗传图谱的稻米外观品质QTL定位. 作物学报, 2018, 44(8):1248-1255.
doi: 10.3724/SP.J.1006.2018.01248 |
PENG Q, LI J L, ZHANG D S, JIANG X, DENG R Y, WU J Q, ZHU S S. QTL mapping for rice appearance quality traits based on a high-density genetic map in different environments. Acta Agronomica Sinica, 2018, 44(8):1248-1255. (in Chinese)
doi: 10.3724/SP.J.1006.2018.01248 |
|
[5] | XIE W B, FENG Q, YU H H, HUANG X H, ZHAO Q, XING Y Z, YU S B, HAN B, ZHANG Q F. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proceedings of the National Academy of the Sciences of the United States of America, 2010, 107(23):10578-10583. |
[6] | 王洪振, 王姝, 邝盼盼, 林政发, 程军, 赵永斌, 李长有, 于长春. DNA分子标记技术及其在植物育种中的应用. 吉林师范大学学报(自然科学版), 2016, 37(1):108-111. |
WANG H Z, WANG S, KUANG P P, LIN Z F, CHENG J, ZHAO Y B, LI C Y, YU C C. DNA molecular marker technology and its application in plant breeding. Jilin Normal University Journal (Natural Science Edition), 2016, 37(1):108-111. (in Chinese) | |
[7] |
HUANG X H, FENG Q, QIAN Q, ZHAO Q, WANG L, WANG A H, GUAN J P, FAN D L, WENG Q J, HUANG T, DONG G J, SANG T, HAN B. High-throughput genotyping by whole-genome resequencing. Genome Research, 2009, 19(6):1068-1076.
doi: 10.1101/gr.089516.108 |
[8] |
HE Q, ZHI H, TANG S, XING L, WANG S Y, WANG H G, ZHANG A Y, LI Y H, GAO M, ZHANG H J, CHEN G Q, DAI S T, LI J X, YANG J J, LIU H F, ZHANG W, JIA Y C, LI S J, LIU J R, QIAO Z J, GUO E H, JIA G Q, LIU J, DIAO X M. QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theoretical and Applied Genetics, 2021, 134(2):557-572.
doi: 10.1007/s00122-020-03714-w |
[9] |
董骥驰, 杨靖, 郭涛, 陈立凯, 陈志强, 王慧. 基于高密度Bin图谱的水稻抽穗期QTL定位. 作物学报, 2018, 44(6):938-946.
doi: 10.3724/SP.J.1006.2018.00938 |
DONG J C, YANG J, GUO T, CHEN L K, CHEN Z Q, WANG H. QTL mapping for heading date in rice using high-density Bin map. Acta Agronomica Sinica, 2018, 44(6):938-946. (in Chinese)
doi: 10.3724/SP.J.1006.2018.00938 |
|
[10] |
ZHOU Z, ZHANG C, ZHOU Y, HAO Z, WANG Z, ZENG X, DI H, LI M, ZHANG D, YONG H, ZHANG S, WENG J, LI X. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines. BMC Genomics, 2016, 17:178.
doi: 10.1186/s12864-016-2555-z |
[11] |
LIU S Y, HUA L, DONG S J, CHEN H Q, ZHU X D, JIANG J E, ZHANG F, LI Y H, FANG X H, CHEN F. OsMAPK6, a mitogen-activated protein kinase, influences rice grain size and biomass production. The Plant Journal, 2015, 84(4):672-681.
doi: 10.1111/tpj.2015.84.issue-4 |
[12] |
XU R, YU H, WANG J, DUAN P, ZHANG B, LI J, LI Y, XU J, LYU J, LI N, CHAI T, LI Y. A mitogen-activated protein kinase phosphatase influences grain size and weight in rice. The Plant Journal, 2018, 95(6):937-946.
doi: 10.1111/tpj.2018.95.issue-6 |
[13] |
XU R, DUAN P G, YU H Y, ZHOU Z K, ZHANG B L, WANG R C, LI J, ZHANG G Z, ZHUANG S S, LYU J, LI N, CHAI T Y, TIAN Z X, YAO S G, LI Y H. Control of grain size and weight by the OsMKKK10-OsMKK4-OsMAPK6 signaling pathway in rice. Molecular Plant, 2018, 11(6):860-873.
doi: 10.1016/j.molp.2018.04.004 |
[14] |
DUAN P G, RAO Y C, ZENG D L, YANG Y L, XU R, ZHANG B L, DONG G J, QIAN Q, LI Y H. SMALL GRAIN 1, which encodes a mitogen-activated protein kinase kinase 4, influences grain size in rice. The Plant Journal, 2014, 77(4):547-557.
doi: 10.1111/tpj.2014.77.issue-4 |
[15] |
GUO T, CHEN K, DONG N Q, SHI C L, YE W W, GAO J P, SHAN J X, LIN H X. GRAIN SIZE AND NUMBER1 negatively regulates the OsMKKK10-OsMKK4-OsMPK6 cascade to coordinate the trade-off between grain number per panicle and grain size in rice. The Plant Cell, 2018, 30(4):871-888.
doi: 10.1105/tpc.17.00959 |
[16] |
SONG X J, HUANG W, SHI M, ZHU M Z, LIN H X. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics, 2007, 39(5):623-630.
doi: 10.1038/ng2014 |
[17] |
HUANG L J, HUA K, XU R, ZENG D L, WANG R C, DONG G J, ZHANG G Z, LU X L, FANG N, WANG D K, DUAN P G, ZHANG B L, LIU Z P, LI N, LUO Y H, QIAN Q, YAO S G, LI Y H. The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice. The Plant Cell, 2021, 33(4):1212-1228.
doi: 10.1093/plcell/koab041 |
[18] |
HUANG K, WANG D, DUAN P, ZHANG B, XU R, LI N, LI Y. WIDE AND THICK GRAIN 1, which encodes an otubain-like protease with deubiquitination activity, influences grain size and shape in rice. The Plant Journal, 2017, 91(5):849-860.
doi: 10.1111/tpj.2017.91.issue-5 |
[19] |
SHI C L, REN Y L, LIU L L, WANG F, ZHANG H, TIAN P, PAN T, WANG Y F, JING R N, LIU T Z, WU F Q, LIN Q B, LEI C L, ZHANG X, ZHU S S, GUO X P, WANG J L, ZHAO Z C, WANG J, ZHAI H Q, CHENG Z J, WAN J M. Ubiquitin specific protease 15 has an important role in regulating grain width and size in rice. Plant Physiology, 2019, 180(1):381-391.
doi: 10.1104/pp.19.00065 |
[20] |
ISHII T, NUMAGUCHI K, MIURA K, YOSHIDA K, THANH P T, HTUN T M, YAMASAKI M, KOMEDA N, MATSUMOTO T, TERAUCHI R. OsLG1 regulates a closed panicle trait in domesticated rice. Nature Genetics, 2013, 45(4):462-465.
doi: 10.1038/ng.2567 |
[21] |
FAN C, XING Y, MAO H, LU T, HAN B, XU C, LI X, ZHANG Q. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics, 2006, 112(6):1164-1171.
doi: 10.1007/s00122-006-0218-1 |
[22] | MAO H L, SUN S Y, YAO J L, WANG C R, YU S B, XU C G, LI X H, ZHANG Q I. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proceedings of the National Academy of the Sciences of the United States of America, 2010, 107(45):19579. |
[23] |
SWAIN, D M, SAHOO R K, SRIVASTAVA V K, TRIPATHY B C, TUTEJA R, TUTEJA N. Function of heterotrimeric G-protein γ subunit RGG1 in providing salinity stress tolerance in rice by elevating detoxification of ROS. Planta, 2016, 245(2):1-17.
doi: 10.1007/s00425-016-2607-2 |
[24] |
MIAO J, YANG Z F, ZHANG D P, WANG Y Z, XU M B, ZHOU L H, WANG J, WU S J, YAO Y L, DU X, GU F F, GONG Z Y, GU M H, LIANG G H, ZHOU Y. Mutation of RGG2, which encodes a type B heterotrimeric G protein γ subunit, increases grain size and yield production in rice. Plant Biotechnology Journal, 2019, 17(3):650-664.
doi: 10.1111/pbi.2019.17.issue-3 |
[25] |
LIU J F, CHEN J, ZHENG X M, WU F Q, LIN Q B, HENG Y Q, TIAN P, CHENG Z J, YU X W, ZHOU K N, ZHANG X, GUO X P, WANG J L, WANG H Y, WAN J M. GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice. Nature Plants, 2017, 3(5):17043.
doi: 10.1038/nplants.2017.43 |
[26] |
LI Y B, FAN C C, XING Y Z, JIANG Y H, LUO L J, SUN L, SHAO D, XU C J, LI X H, XIAO J H, HE Y Q, ZHANG Q F. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 2011, 43(12):1266-1269.
doi: 10.1038/ng.977 |
[27] |
SHI C L, DONG N Q, GUO T, YE W W, SHAN J X, LIN H X. A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway. The Plant Journal, 2020, 103(3):1174-1188.
doi: 10.1111/tpj.v103.3 |
[28] |
HU J, WANG Y X, FANG Y X, ZENG L J, XU J, YU H P, SHI Z Y, PAN J J, ZHANG D, KANG S J, ZHU L, DONG G J, GUO L B, ZENG D, ZHANG G H, XIE L H, XIONG G S, LI J Y, QIAN Q. A rare allele of GS2 enhances grain size and grain yield in rice. Molecular Plant, 2015, 8(10):1455-1465.
doi: 10.1016/j.molp.2015.07.002 |
[29] |
DUAN P G, NI S, WANG J M, ZHANG B L, XU R, WANG Y X, CHEN H Q, ZHU X O, LI Y H. Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice. Nature Plants, 2015, 2(1):15203.
doi: 10.1038/nplants.2015.203 |
[30] |
CHE R H, TONG H N, SHI B H, LIU Y Q, FANG S R, LIU D P, XIAO Y H, HU B, LIU L C, WANG H R. Control of grain size and rice yield by GL2-mediated brassinosteroid responses. Nature Plants, 2015, 2(1):15195.
doi: 10.1038/nplants.2015.195 |
[31] |
WANG S K, WU K, YUAN Q B, LIU X Y, LIU Z B, LIN X Y, ZENG R Z, ZHU H T, DONG G J, QIAN Q, ZHANG G Q, FU X D. Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics, 2012, 44(8):950-954.
doi: 10.1038/ng.2327 |
[32] |
SI L Z, CHEN J Y, HUANG X H, GONG H, LUO J H, HOU Q Q, ZHOU T Y, LU T T, ZHU J J, SHANGGUAN Y Y, CHEN E W, GONG C X, ZHAO Q, JING Y F, ZHAO Y, LI Y, CUI L L, FAN D L, LU Y Q, WENG Q J, WANG Y C, ZHAN Q L, LIU K Y, WEI X H, AN K, AN G, HAN B. OsSPL13 controls grain size in cultivated rice. Nature Genetics, 2016, 48(4):447-456.
doi: 10.1038/ng.3518 |
[33] |
ZHAO D S, LI Q F, ZHANG C Q, ZHANG C, YANG Q Q, PAN L X, REN X Y, LU J, GU M H, LIU Q Q. GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality. Nature Communications, 2018, 9(1):1240.
doi: 10.1038/s41467-018-03616-y |
[34] |
LIU Q, HAN R, WU K, ZHANG J Q, YE Y F, WANG S S, CHEN J F, PAN Y J, LI Q, XU X P, ZHOU J W, TAO D Y, WU Y J, FU X D. G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nature Communications, 2018, 9(1):852.
doi: 10.1038/s41467-018-03047-9 |
[35] |
ZHU X, ZHANG S, CHEN Y, MOU C, HUANG Y, LIU X, JI J, YU J, HAO Q, YANG C, CAI M, NGUYEN T, SONG W, WANG P, DONG H, LIU S, JIANG L, WAN J. Decreased grain size1, a C3HC4-type RING protein, influences grain size in rice (Oryza sativa L.). Plant Molecular Biology, 2021, 105(4):405-417.
doi: 10.1007/s11103-020-01096-7 |
[36] | LEI M, LI H H, ZHANG L Y, WANG J K. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop Journal, 2015(3):103-117. |
[37] |
MCCOUCH S R. Gene nomenclature system for rice. Rice, 2008, 1(1):72-84.
doi: 10.1007/s12284-008-9004-9 |
[38] |
YU H H, XIE W B, LI J, ZHOU F S, ZHANG Q F. A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnology Journal, 2013, 12(1):28-37.
doi: 10.1111/pbi.2013.12.issue-1 |
[39] | BAYER P E. Skim-based genotyping by sequencing using a double haploid population to call SNPs, infer gene conversions, and improve genome assemblies//EDWARDS D. Plant Bioinformatics: Methods and Protocols. New York: Springer New York Press, 2016: 285-292. |
[40] |
YANG J, SUN K, LI D X, LUO L X, LIU Y Z, HUANG M, YANG C L, LIU H, WANG H, CHEN Z Q, GUO T. Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq. BMC Genomics, 2019, 20:355.
doi: 10.1186/s12864-019-5741-y |
[41] |
YU H H, XIE W B, WANG J, XING Y Z, XU C G, LI X H, XIAO J H, ZHANG Q F. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE, 2011, 6(3):e17595.
doi: 10.1371/journal.pone.0017595 |
[42] |
YANG J, GUO Z H, LUO L X, GAO Q L, XIAO W M, WANG J F, WANG H, CHEN Z Q, GUO T. Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq. The Crop Journal, 2021, 9(2):360-371.
doi: 10.1016/j.cj.2020.08.010 |
[43] | DU Z X, ZHOU H, LI J B, BAO J Z, TU H, ZENG C H, WU Z, FU H H, XU J, ZHOU D H, ZHU C L, FU J R, HE H H. qTGW12a, a naturally varying QTL, regulates grain weight in rice. Theoretical and Applied Genetics, 2021. https://doi.org/10.1007/s00122-021-03857-4. |
[44] |
PONCE K, ZHANG Y, GUO L B, LENG Y J, YE G Y. Genome-wide association study of grain size traits in indica rice multiparent advanced generation intercross (MAGIC) population. Frontiers in Plant Science, 2020, 11:395.
doi: 10.3389/fpls.2020.00395 |
[45] |
LO S F, CHENG M L, HSING Y C, CHEN Y S, LEE K W, HONG Y F, HSIAO Y, HSIAO A S, CHEN P J, WONG L I, CHEN N C, REUZEAU C, HO T D, YU S M. Rice Big Grain 1 promotes cell division to enhance organ development, stress tolerance and grain yield. Plant Biotechnology Journal, 2020, 18(9):1969-1983.
doi: 10.1111/pbi.v18.9 |
[46] |
FAN C C, YU S B, WANG C R, XING Y Z. A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theoretical and Applied Genetics, 2009, 118(3):465-472.
doi: 10.1007/s00122-008-0913-1 |
[47] |
QI P, LIN Y S, SONG X J, SHEN J B, HUANG W, SHAN J X, ZHU M Z, JIANG L W, GAO J P, LIN H X. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Research, 2012, 22(12):1666-1680.
doi: 10.1038/cr.2012.151 |
[48] | ZHANG X J, WANG J F, HUANG J, LAN H X, WANG C L, YIN C F, WU Y Y, TANG H J, QIAN Q, LI J Y. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of the Sciences of the United States of America, 2012, 109(52):21534-21539. |
[49] |
WANG Y, XIONG G, HU J, JIANG L, YU H, XU J, FANG Y, ZENG L, XU E, XU J, YE W, MENG X, LIU R, CHEN H, JING Y, WANG Y, ZHU X, LI J, QIAN Q. Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nature Genetics, 2015, 47(8):944-948.
doi: 10.1038/ng.3346 |
[50] |
WANG S, LI S, LIU Q, WU K, ZHANG J, WANG S, WANG Y, CHEN X, ZHANG Y, GAO C, WANG F, HUANG H, FU X. The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature Genetics, 2015, 47(8):949-954.
doi: 10.1038/ng.3352 |
[51] |
WU W, LIU X, WANG M, MEYER R S, LUO X, NDJIONDJOP M N, TAN L, ZHANG J, WU J, CAI H, SUN C, WANG X, WING R A, ZHU Z. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 2017, 3:17064.
doi: 10.1038/nplants.2017.64 |
[52] |
YING J Z, MA M, BAI C, HUANG X H, LIU J L, FAN Y Y, SONG X J. TGW3, a major QTL that negatively modulates grain length and weight in rice. Molecular Plant, 2018, 11(5):750-753.
doi: 10.1016/j.molp.2018.03.007 |
[53] |
XIA D, ZHOU H, LIU R J, DAN W H, LI P B, WU B, CHEN J X, WANG L Q, GAO G J, ZHANG Q L, HE Y Q. GL3.3, a novel QTL encoding a GSK3/SHAGGY-like kinase, epistatically interacts with GS3 to produce extra-long grains in rice. Molecular Plant, 2018, 11(5):754-756.
doi: 10.1016/j.molp.2018.03.006 |
[54] |
ZHANG Y P, ZHANG Z Y, SUN X M, ZHU X Y, LI B, LI J J, GUO H F, CHEN C, PAN Y H, LIANG Y T, XU Z J, ZHANG H L, LI Z C. Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica. Plant Biotechnology Journal, 2019, 17(8):1547-1559.
doi: 10.1111/pbi.2019.17.issue-8 |
[55] |
DUAN P G, XU J S, ZENG D L, ZHANG B L, GENG M F, ZHANG G Z, HUANG K, HUANG L J, XU R, GE S, QIAN Q, LI Y H. Natural variation in the promoter of GSE5 contributes to grain size diversity in rice. Molecular Plant, 2017, 10(5):685-694.
doi: 10.1016/j.molp.2017.03.009 |
[56] |
SHOMURA A, IZAWA T, EBANA K, EBITANI T, KANEGAE H, KONISHI S, YANO M. Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics, 2008, 40(8):1023-1028.
doi: 10.1038/ng.169 |
[57] |
WANG S S, WU K, QIAN Q, LIU Q, LI Q, PAN Y J, YE Y F, LIU X Y, WANG J, ZHANG J Q, LI S, WU Y J, FU X D. Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Research, 2017, 27(9):1142-1156.
doi: 10.1038/cr.2017.98 |
[58] |
ISHIMARU K, HIROTSU N, MADOKA Y, MURAKAMI N, HARA N, ONODERA H, KASHIWAGI T, UJIIE K, SHIMIZU B-I, ONISHI A, MIYAGAWA H, KATOH E. Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nature Genetics, 2013, 45(6):707-711.
doi: 10.1038/ng.2612 |
[59] | SONG X J, KUROHA T, AYANO M, FURUTA T, NAGAI K, KOMEDA N, SEGAMI S, MIURA K, OGAWA D, KAMURA T, SUZUKI T, HIGASHIYAMA T, YAMASAKI M, MORI H, INUKAI Y, WU J Z, KITANO H, SAKAKIBARA H, JACOBSEN S E, ASHIKARI M. Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(1):76-81. |
[60] |
SEGAMI S, KONO I, ANDO T, YANO M, IWASAKI Y. Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice. Rice, 2012, 5(1):4.
doi: 10.1186/1939-8433-5-4 |
[61] |
WANG C R, CHEN S, YU S B. Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theoretical and Applied Genetics, 2011, 122:905-913.
doi: 10.1007/s00122-010-1497-0 |
[62] | 张亚东, 张颖慧, 董少玲, 陈涛, 赵庆勇, 朱镇, 周丽慧, 姚姝, 赵凌, 于新, 王才林. 特大粒水稻材料粒型性状的QTL检测. 中国水稻科学, 2013, 27(2):122-128. |
ZHANG Y D, ZHANG Y H, DONG S L, CHEN T, ZHAO Q Y, ZHU Z, ZHOU L H, YAO S, ZHAO L, YU X, WANG C L. Identification of QTL for rice grain traits based on an extra-large grain material. Chinese Journal of Rice Science, 2013, 27(2):122-128. (in Chinese) | |
[63] |
JIANG Y H, BAO L, JEONG S Y, KIM S K, XU C G, LI X H, ZHANG Q F. XIAO is involved in the control of organ size by contributing to the regulation of signaling and homeostasis of brassinosteroids and cell cycling in rice. The Plant Journal, 2012, 70(3):398-408.
doi: 10.1111/tpj.2012.70.issue-3 |
[64] |
RUAN B P, SHANG L G, ZHANG B, HU J, WANG Y X, LIN H, ZHANG A P, LIU C L, PENG Y L, ZHU L, REN D Y, SHEN L, DONG G J, ZHANG G H, ZENG D L, GUO L B, QIAN Q, GAO Z Y. Natural variation in the promoter of TGW2 determines grain width and weight in rice. New Phytologist, 2020, 227(2):629-640.
doi: 10.1111/nph.v227.2 |
[65] |
LYU J, WANG D K, DUAN P G, LU Y P, HUANG K, ZENG D L, ZHANG L M, DONG G J, LI Y J, XU R, ZHANG B L, HUANG X H, LI N, WANG Y C, QIAN Q, LI Y H. Control of grain size and weight by the GSK2-LARGE1/OML4 pathway in rice. The Plant Cell, 2020, 32(6):1905-1918.
doi: 10.1105/tpc.19.00468 |
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