Crops ›› 2021, Vol. 37 ›› Issue (6): 36-45.doi: 10.16035/j.issn.1001-7283.2021.06.006

Previous Articles     Next Articles

Detection of QTL for Root Length and Bud Length at Germination Stage in Low Temperature Using CSSLs in Rice (Oryza sativa)

Yu Meixia1(), Deng Haodong1(), Tan Jing’ai1, Song Guiting1, Wu Guangliang1, Chen Liping1, Liu Ruiqi1, Zhou Andong1, He Haohua1,2, Bian Jianmin1,2()   

  1. 1Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education/Jiangxi Province, Nanchang 330045, Jiangxi, China
    2Jiangxi Super Rice Engineering Technology Research Center, Nanchang 330045, Jiangxi, China
  • Received:2020-12-14 Revised:2021-01-01 Online:2021-12-15 Published:2021-12-16
  • Contact: Bian Jianmin E-mail:1873831573@qq.com;1303051137@qq.com;jmbian81@126.com

Abstract:

The growth and development of roots and shoots have an important influence on yield. In order to explore the quantitative trait loci (QTL) affecting root length and bud length in bud bursting period under different temperature treatments, the chromosome segment substitution lines (CSSLs) population of 9311 (recipient)/Nipponbare (donor) used as the experimental materials. The germinated seeds were treated at 15℃ for seven days and then recovery grew at 25℃ for seven days. During the recovered period, 10 seeds were randomly selected to measure root length and bud length. After the treatments, the QTL associated with root length and bud length were detected by the CSSLs population. Under 15℃ treatments, nine QTLs affecting root length were detected, the range of contribution rates was 8.65%-24.35%. qRL15T7.2, and qRL15T10.3 were repeatedly detected at different periods of root growth; nine QTL affecting the bud length at 15℃ were detected, and the explained phenotypic variations were from 1.73% to 28.89%, qBL15T6, qBL15T7, qBL15T9, and qBL15T10 were repeatedly detected at different periods of bud growth; Under 25℃ treatments, nine QTL affecting the root length were located, the range of contribution rates was 1.73%-28.89%, qRL25T7, qRL25T9.3, qRL25T10, and qRL25T12 were repeatedly detected; five QTL affecting bud length were detected, and the contribution rates were 0.58%-38.26%, only qBL25T3.3 was repeatedly detected at different periods of bud growth. Four recombination bin markers were located on chromosomes 2, 7, 9, 10, also affected different traits at the same temperature or different traits at different temperatures. The results showed that the QTL affecting root length and bud length were different under different treatments. The results suggest that the genetic mechanism of controlling the growth of roots and buds at the bud stage of rice under low temperature may be different from under normal temperature.

Key words: Rice, Root length, Bud length, QTL, CSSLs

Table 1

The bin marker numbers and genetic distance between adjacent bins Mb"

染色体
Chromosome
标记数目
Number
of marker
平均距离
Mean
distance
最小距离
Minimum
distance
最大距离
Maximum
distance
1 68 0.64 0.10 3.40
2 64 0.56 0.10 2.90
3 59 0.62 0.10 3.45
4 69 0.52 0.10 4.70
5 47 0.64 0.10 3.60
6 37 0.82 0.10 12.85
7 52 0.57 0.10 2.30
8 34 0.84 0.15 8.90
9 33 0.68 0.15 1.85
10 59 0.40 0.10 1.00
11 76 0.38 0.10 2.50
12 57 0.47 0.10 2.95

Fig.1

Graphical genotypes of the CSSLs Black indicates genotypes for Nipponbare, white indicates genotypes for 9311"

Table 2

Phenotype analysis of root length and bud length under two temperatures of their parents and CSSL population"

温度
Temperature
性状
Trait
生长天数
Growth
day (d)
亲本Parents CSSL群体CSSL population
9311
(cm)
日本晴
Nipponbare (cm)
均值
Mean (cm)
标准误
Standard error
偏度
Skewness
峰度
Kurtosis
最小值
Minimum (cm)
最大值
Maximum (cm)
15°C 根长 1 2.27 1.62** 2.54 1.03 0.55 -0.38 0.58 4.90
2 2.69 2.00* 3.57 1.12 0.27 -0.78 1.18 5.97
3 2.95 2.43 4.33 1.23 0.02 -0.67 1.23 6.93
4 2.87 2.33 4.87 1.28 -0.13 -0.60 1.46 7.81
5 2.70 2.43 5.34 1.28 -0.68 1.54 0.00 8.08
6 2.60 2.33 5.89 1.33 -1.06 2.46 0.00 8.48
7 2.73 2.51 6.21 1.39 -1.12 2.74 0.00 9.41
芽长 1 2.45 2.01 1.66 0.59 0.95 -0.37 0.90 3.16
2 3.07 3.08 2.92 0.48 -0.16 -0.11 1.67 3.88
3 3.38 3.40 3.93 0.46 -1.39 3.55 2.05 4.87
4 3.59 3.46 4.50 0.48 -1.53 5.40 2.41 5.60
5 3.67 4.29 4.75 0.63 -4.01 27.71 0.00 5.85
6 3.69 5.25** 5.04 0.71 -2.87 23.19 0.00 7.66
7 4.13 5.53** 5.56 0.91 -1.37 12.57 0.00 9.07
25°C 根长 1 0.43 0.00** 0.40 0.33 0.32 -1.21 0.00 1.07
2 1.40 0.28** 1.83 0.90 0.05 -1.11 0.20 3.62
3 2.74 1.61** 3.18 1.17 -0.06 -0.92 0.92 5.70
4 3.75 2.49** 3.96 1.14 -0.31 -0.79 1.47 6.21
5 4.50 3.88 4.75 1.22 -0.44 -0.77 2.08 6.94
6 5.49 4.60 5.24 1.17 -0.62 -0.22 1.87 7.28
7 6.26 5.71 5.74 1.13 -0.46 -0.42 2.64 7.81
芽长 1 0.20 0.00 0.25 0.15 4.44 25.49 0.08 1.18
2 0.82 0.25 0.81 0.29 2.48 10.67 0.39 2.33
3 1.40 0.73* 1.58 0.43 0.68 0.32 0.90 3.06
4 2.44 1.02** 2.29 0.54 0.27 -0.69 1.19 3.77
5 3.09 2.06** 3.14 0.63 0.44 0.92 1.62 5.55
6 3.72 2.76** 3.76 0.61 -0.08 -0.48 2.26 5.12
7 4.02 3.68 4.19 0.56 -0.55 0.27 2.43 5.29

Fig.2

Phenotypic distribution of CSSL population at 15℃ and 25℃"

Table 3

QTL mapping for root length and bud length under two temperatures using CSSL population at different stages of sprout growth"

温度
Temperature
性状
Trait
生长天数
Growth day (d)
染色体
Chromosome
QTL 连锁标记
Linkage marker
LOD值
LOD value
加性效应
Additive effect
贡献率
Contribution rate (%)
15°C 根长 1 2 qRL15T2.1 chr2-bin113 3.07 0.69 11.42
7 7 qRL15T7.1 chr7-bin385 3.23 -1.15 8.66
4 qRL15T7.2 chr7-bin387 2.66 -1.03 8.68
6 3.84 -1.25 11.92
3 qRL15T7.3 chr7-bin393 3.01 -0.75 9.58
1 10 qRL15T10.1 chr10-bin501 2.75 -0.61 10.17
4 qRL15T10.2 chr10-bin504 4.08 -1.16 13.73
3 qRL15T10.3 chr10-bin505 4.41 -1.28 14.46
6 5.36 -1.50 17.17
7 qRL15T10.4 chr10-bin507 8.27 -2.21 24.36
5 qRL15T10.5 chr10-bin510 4.12 -1.12 15.61
芽长 1 1 qBL15T1 chr1-bin11 5.24 0.66 17.05
1 2 qBL15T2 chr2-bin113 3.59 0.41 11.08
3 3 qBL15T3.1 chr3-bin135 4.51 -0.86 13.82
3 qBL15T3.2 chr3-bin154 2.79 -0.47 8.22
5 6 qBL15T6 chr6-bin339 25.36 2.31 19.50
6 16.24 1.92 14.72
2 7 qBL15T7 chr7-bin393 2.70 -0.30 10.60
3 5.55 -0.35 17.37
4 3.67 -0.35 13.69
5 8 qBL15T8 chr8-bin425 3.68 0.69 1.73
6 9 qBL15T9 chr9-bin448 3.27 0.61 2.22
7 2.96 0.95 11.54
4 10 qBL15T10 chr10-bin507 2.57 -0.43 8.55
5 31.09 -2.22 26.92
6 27.73 -2.19 28.90
25°C 根长 4 1 qRL25T1 chr1-bin52 2.93 -0.92 6.03
5 7 qRL25T7 chr7-bin345 3.07 -0.73 6.04
6 3.56 -0.94 10.76
5 8 qRL25T8.1 chr8-bin415 2.56 -1.06 5.22
4 qRL25T8.2 chr8-bin430 5.13 -1.25 11.08
6 9 qRL25T9.1 chr9-bin439 2.83 -0.72 8.43
5 qRL25T9.2 chr9-bin448 4.37 -1.16 9.24
2 qRL25T9.3 chr9-bin459 3.32 -0.68 10.24
3 3.31 -0.93 12.82
4 5.84 -0.96 12.80
5 4.28 -0.82 9.03
4 10 qRL25T10 chr10-bin495 4.47 -0.83 9.51
5 5.84 -0.98 12.74
6 3.10 -0.81 9.28
4 12 qRL25T12 chr12-bin599 3.11 -0.95 6.43
5 4.47 -1.18 9.48
芽长 1 3 qBL25T3.1 chr3-bin136 45.91 -0.46 29.14
1 qBL25T3.2 chr3-bin138 51.60 0.47 38.26
1 qBL25T3.3 chr3-bin147 21.86 0.46 7.53
2 7.17 0.77 25.74
3 2.70 0.75 10.59
5 qBL25T3.4 chr3-bin186 3.52 1.22 13.60
1 11 qBL25T11 chr11-bin596 2.59 0.06 0.58

Fig.3

Distribution of QTL related root length and bud length on genetic map under two temperature treatments of CSSL population"

Table 4

Chromosomal markers corresponding to regions with pleiotropic effects on traits"

染色体
Chromosome
连锁标记
Linkage
marker
物理位置
Physical location
(Mb)
影响性状Affected trait
15℃ 25℃
2 bin113 19.75~20.75 根长、芽长
7 bin393 28.25~28.70 根长、芽长
9 bin448 11.15~12.45 芽长 根长
10 bin507 15.75~17.20 根长、芽长
[1] Zhang Z Y, Li J J, Pan Y H, et al. Natural variation in CTB4a enhances rice adaptation to cold habitats. Nature Communications, 2017(8):14788.
[2] 刘次桃, 王威, 毛毕刚, 等. 水稻耐低温逆境研究:分子生理机制及育种展望. 遗传, 2018, 40(3):171-185.
[3] Groot T T, Bodegom V P, Meijer H, et al. Gas Transport through the root-shoot transition zone of rice tillers. Plant and Soil, 2005, 277(1):107-116.
doi: 10.1007/s11104-005-0435-4
[4] 韩龙植, 乔永利, 曹桂兰, 等. 水稻生长早期耐冷性QTL分析. 中国水稻科学, 2005(2):122-126.
[5] 杨洛淼, 王敬国, 刘化龙, 等. 寒地粳稻发芽期和芽期的耐冷性QTL定位. 作物杂志, 2014(6):44-51.
[6] Andaya V C, Tai T H. Fine mapping of the qCTS12 locus,a major QTL for seedling cold tolerance in rice. Theoretical and Applied Genetics, 2006, 113(3):467-475.
pmid: 16741739
[7] Fujino K, Sekiguchi H. Origins of functional nucleotide polymorphisms in a major quantitative trait locus,qLTG3-1,controlling low-temperature germinability in rice. Plant Molecular Biology, 2011, 75(1/2):1-10.
doi: 10.1007/s11103-010-9697-1
[8] Li J L, Pan Y H, Guo H F, et al. Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice. Theoretical and Applied Genetics, 2018, 131(1):157.
doi: 10.1007/s00122-017-2992-3
[9] Shi Y T, Yang S H. COLD1:a cold sensor in rice. Science China Life Sciences, 2015, 58(4):409-410.
doi: 10.1007/s11427-015-4831-6
[10] Zhou L, Zeng Y W, Zheng W W, et al. Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line. Theoretical and Applied Genetics, 2010, 121(5):895-905.
doi: 10.1007/s00122-010-1358-x pmid: 20512559
[11] Steele K A, Price A H, Shashidhar H E, et al. Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theoretical and Applied Genetics, 2006, 112(2):208-221.
pmid: 16208503
[12] Shimizu A, Kato K, Komatsu A, et al. Genetic analysis of root elongation induced by phosphorus deficiency in rice (Oryza sativa L.):fine QTL mapping and multivariate analysis of related traits. Theoretical and Applied Genetics, 2008, 117(6):987-996.
doi: 10.1007/s00122-008-0838-8
[13] Mitsuhiro O, Wataru T, Takeshi E, et al. Fine-mapping of qRL6.1,a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions. Theoretical and Applied Genetics, 2010, 121(3):535-547.
doi: 10.1007/s00122-010-1328-3 pmid: 20390245
[14] Wang H M, Xu X M, Zhan X D, et al. Identification of qRL7,a major quantitative trait locus associated with rice root length in hydroponic conditions. Breeding Science, 2013, 63(3):267-274.
doi: 10.1270/jsbbs.63.267
[15] 徐晓明, 张迎信, 王会民, 等. 一个水稻根长QTL qRL4的分离鉴定. 中国水稻科学, 2016, 30(4):363-370.
[16] 赵春芳, 张亚东, 陈涛, 等. 低磷胁迫下水稻苗期根长性状的QTL定位. 华北农学报, 2013, 28(6):6-10.
[17] Redona E D, Mackill D J. Mapping quantitative trait loci for seedling vigor in rice using RFLPs. Theoretical and Applied Genetics, 1996, 92(3/4):395-402.
doi: 10.1007/BF00223685
[18] Fukuda A, Terao T. QTLs for shoot length and Chlorophyll content of rice seedlings grown under low-temperature conditions,using a cross between Indica and Japonica cultivars. Plant Production Science, 2015, 18(2):128-136.
doi: 10.1626/pps.18.128
[19] Zhang Z H, Yu S B, Yu T, et al. Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.). Field Crops Research, 2004, 91(2):161-170.
doi: 10.1016/j.fcr.2004.06.004
[20] 班超, 张晓玲, 穆平. 水稻根系性状QTL的整合、分类和真实性分析. 中国农学通报, 2009, 25(19):20-25.
[21] Meng L, Li H H, Zhang L Y, et al. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in bi-parental populations. The Crop Journal, 2015(3):269-283.
[22] Li H H, Ye G Y, Wang J K. A modified algorithm for the improvement of composite interval mapping. Genetics, 2007, 175(1):361-374.
doi: 10.1534/genetics.106.066811
[23] McCouch S R. Committee on gene symbolization,nomenclature and linkage,rice genetics cooperative. Rice, 2008, 1(1):72-84.
doi: 10.1007/s12284-008-9004-9
[24] 王存虎, 刘东, 许锐能, 等. 大豆叶柄角的QTL定位分析. 作物学报, 2020, 46(1):9-19.
[25] 陈利华, 万杉. 不同温度条件下水稻种子活力QTL的定位分析. 武汉植物学研究, 2005, 23(2):125-130.
[26] 代贵金, 华泽田, 陈温福, 等. 杂交粳稻、常规粳稻、旱稻及籼稻根系特征比较. 沈阳农业大学学报, 2008, 39(5):515-519.
[27] 蔡昆争, 骆世明, 段舜山. 水稻群体根系特征与地上部生长发育和产量的关系. 华南农业大学学报, 2005, 26(2):1-4.
[28] Fujino K, Sekiguchi H, Sato T, et al. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theoretical and Applied Genetics, 2004, 108(5):794-799.
pmid: 14624339
[29] Miura K, Lin S Y, Yano M, et al. Mapping quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Breeding Science, 2001, 51(4):293-299.
doi: 10.1270/jsbbs.51.293
[30] Courtois B, Shen L, Petalcorin W, et al. Locating QTLs controlling constitutive root traits in the rice population IAC 165×Co39. Euphytica, 2003, 134(3):335-345.
doi: 10.1023/B:EUPH.0000004987.88718.d6
[31] Zheng H G, Babu R C, Pathan M S, et al. Quantitative trait loci for root-penetration ability and root thickness in rice:comparison of genetic backgrounds. Genome, 2000, 43(1):53-61.
pmid: 10701113
[32] 徐吉臣, 李晶昭, 郑先武, 等. 苗期水稻根部性状的QTL定位. 遗传学报, 2001, 28(5):433-439.
[33] Uga Y, Okuno K, Yano M. QTLs underlying natural variation in stele and xylem structures of rice root. Breeding Science, 2008, 58(1):7-14.
doi: 10.1270/jsbbs.58.7
[34] Ikeda H, Kamoshita A, Manabe T. Genetic analysis of rooting ability of transplanted rice (Oryza sativa L.) under different water conditions. Journal of Experimental Botany, 2007, 58(2):309-318
pmid: 17075079
[35] Li W X, Zhao H J, Pang W Q, et al. Seed-specific silencing of OsMRP5 reduces seed phytic acid and weight in rice. Transgenic Research, 2014, 23(4):585-599.
doi: 10.1007/s11248-014-9792-1
[36] Yukihiro I, Fumiko K, Kazuma H, et al. Fatty acid elongase is required for shoot development in rice. Plant Journal, 2011, 66(4):680-688.
doi: 10.1111/j.1365-313X.2011.04530.x
[37] Zhao Y, Jiang C H, Rehman R, et al. Genetic analysis of roots and shoots in rice seedling by association mapping. Genes and Genomics, 2019, 41(1):95-105.
doi: 10.1007/s13258-018-0741-x pmid: 30242741
[1] Tang Gang, Liao Ping, Sui Feng, Lü Weisheng, Zhang Jun, Zeng Yongjun, Huang Shan. Effects of Moldboard Plow Tillage under all Straw Returning in Late Rice Season on Greenhouse Gas Emissions and Yield in Double Rice-Cropping System [J]. Crops, 2021, 37(6): 101-107.
[2] Zhou Qiancong, Chen Le, Luo Kang, Liu Mengjie, Song Yongping, Xie Xiaobing, Zeng Yongjun. Effects of Nitrogen Panicle Fertilizer Management on Yield and Quality of Hybrid Late Japonica Rice [J]. Crops, 2021, 37(6): 129-133.
[3] Wang Qi, Li Meijuan, Zhang Jia’en, Tang Jiaxin, Zeng Wenjing, Zhou Lei, Yang Qingxin, Jiang Mingmin, Wu Jiayuan, Luo Mingzhu. Effects of Rice-Fish Co-Culture on Chlorophyll Fluorescence Characteristics and Yield in Rice [J]. Crops, 2021, 37(6): 145-151.
[4] Li Yang, Yang Xiaolong, Wang Benfu, Zhang Zhisheng, Chen Shaoyu, Li Jinlan, Cheng Jianping. Effects of Main Season Stubble Height on Ratoon Season Yield and Rice Quality [J]. Crops, 2021, 37(6): 164-170.
[5] Li Xu, Fu Lidong, Wang Yu, Sui Xin, Ren Hai, Lü Xiaohong, Ma Chang, Du Meng, Mao Ting. Effects of Genetic Interaction between DEP1 and NRT1.1B on Nitrogen Use in Rice [J]. Crops, 2021, 37(6): 22-27.
[6] Yu Julong, Zhang Guo, Zhao Laicheng, Yao Kebing, Luo Guanghua, Fang Jichao, Zhang Jianhua, Jiao Yang, Shu Zhaolin. Control Effects of Different Seed Treatments on the Rice Leaf Folder under Machine-Planting Condition [J]. Crops, 2021, 37(6): 224-229.
[7] Zhang Jun, Deng Aixing, Shang Ziyin, Tang Zhiwei, Yan Shengji, Zhang Weijian. Innovative Rice Cropping for Higher Yield and Less CH4 Emission under Crop Straw Incorporation [J]. Crops, 2021, 37(6): 230-235.
[8] Su Daiqun, Chen Liang, Li Feng, Wu Qi, Bai Junjie, Zou Detang, Wang Jingguo, Liu Hualong, Zheng Hongliang. Identification of New Heading Date QTLs Using High Density Genetic Map in Rice [J]. Crops, 2021, 37(6): 58-61.
[9] Zhou Qiyun, Zheng Chongyi, Jing Yongfeng, Liu Yongjun, Peng Shuguang, Chen Tao, Liu Zhixuan, Hu Ruiwen, Zhou Qingming, Li Juan. Study on Soil Organic Matter Content and Its Relationship with Nitrogen, Phosphorus and Potassium in Different Soil Layers of Rice-Growing Tobacco Areas in Southern Hunan [J]. Crops, 2021, 37(5): 114-119.
[10] Shi Nan, Gao Zhiqiang, Hu Haiyan, Chen Chongyi, Wen Shuangya. The Effects of Ordered Machine Thickening and Reducing Fertilizer on Yield and Partial Fertilizer Productivity of Hybrid Rice [J]. Crops, 2021, 37(5): 128-133.
[11] Tang Zhiqiang, Zhang Liying, He Na, Ma Zuobing, Zhao Mingzhu, Wang Changhua, Zheng Wenjing, Yin Yong’an, Wang Hui. Effects of Mechanical Direct Dry Seeding on Rice Growth, Photosynthetic Characteristics and Yield [J]. Crops, 2021, 37(5): 87-94.
[12] Pan Gaofeng, Wang Benfu, Chen Bo, Fang Zhenbing, Zhao Shasha, Tian Yonghong. Effects of Seeding Date on Yield, Growth Period and Utilization of Temperature and Sunshine of Different Types of Japonica Rice in North Central of Hubei Province [J]. Crops, 2021, 37(4): 105-111.
[13] Tong Tianyi, Cai Jianxuan, Zhang Jisheng, Li Lin, Ma Lin, He Roujing, Tang Xiangru. Effects of Fertilizer Types on Yield, Quality and Aroma of Fragrant Rice [J]. Crops, 2021, 37(4): 152-158.
[14] Wu Ke, Xie Huimin, Liu Wenqi, Mo Bingmao, Wei Guoliang, Lu Xian, Li Zhuanglin, Deng Senxia, Wei Shanqing, Liang He, Jiang Ligeng. Effects of Nitrogen, Phosphorus and Potassium Fertilizer on Rice Grain Yield and Yield Components in Double Cropping Rice Area of Southern China [J]. Crops, 2021, 37(4): 178-183.
[15] Ling Chen, Liu Hong, Yang Zhe, Huang Zhanquan, Chen Mengqiang, Rao Dehua, Xu Zhenjiang. Effects of Double-Cropping Rice Cultivation on the Expression of Quantitative Characteristics of Rice DUS Testing Example Varieties [J]. Crops, 2021, 37(4): 18-25.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!