Detection and Analysis of Dynamic Quantitative Trait Loci at Three Years for Seed Storability in Rice (Oryza sativa)

doi:10.11983/CBB18188

Abstract

Abstract: Seed storability is one of the most important special agronomic traits of grain crops, which has great significance for seed production and germplasm conservation. In this study, we obtained a set of recombinant inbred lines (RILs), containing 180 lines and 223 molecular markers for a genetic map, derived from the cross between Longdao5 (LD5) and Zhongyouzao8 (ZYZ8). The set was used to identify quantitative trait loci (QTL) for seed storability traits under natural aging (higher temperature and humidity) at 1, 2 and 3 years after rice harvest. Then the germination rates of seeds at different storage stages were compared and identified by dynamic QTLs. The germination rate of the parents (the germination rate of LD5 was significantly lower than ZYZ8 under different storage stages) and RILs population was significant different under different storage stages, with a significant correlation of germination rate under different storage stages. A total of 17 QTLs were detected to control seed storability; 5, 4 and 3 QTLs were detected for 3 natural aging stages; and 5 dynamic conditional QTLs were detected; these QTLs explained 5.60% to 32.76% of the phenotypic variation, with an additive effect of -16.78% to 16.95%. Among these QTLs, 4 major clusters qSSC2, qSSC6, qSSC7 and qSSC8 were stably and reliably detected under 3 environments; the remaining QTLs were expressed in a single environment. qSSC6 reduced the germination rate. We detected 26 pairs of epistatic interaction sites. The major QTLs qSS1 and qSS4 were also involved in the epistasis effect, so epistatic interaction was an important genetic component for seed storability. These results will provide information for genetic analysis and related QTL fine mapping and will also enrich the gene resources for molecular marker-assisted selection of seed storability.

Key words: rice, natural aging, seed storability, QTL analysis, epistasis interaction

Jin Liu,Xiaoyun Yao,Liqin Yu,Hui Li,Huiying Zhou,Jiayu Wang,Maomao Li. Detection and Analysis of Dynamic Quantitative Trait Loci at Three Years for Seed Storability in Rice (Oryza sativa)[J]. Chinese Bulletin of Botany, 2019, 54(4): 464-473.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.chinbullbotany.com/EN/10.11983/CBB18188

https://www.chinbullbotany.com/EN/Y2019/V54/I4/464

Figures/Tables 7

References 50

[1]	龚继平, 吴方喜, 吴跃进, 郑家团, 黄庭旭, 王乌齐, 张建福, 谢华安 ( 2008). 籼稻脂肪酶基因的遗传分析及定位. 中国水稻科学 22, 125-130.
[2]	贺梅, 张文忠, 宋冬明, 王嘉宇, 谢文孝 ( 2007). 不同储藏温度及储藏时间对稻米品质的影响. 沈阳农业大学学报 38, 472-477.
[3]	江川, 王金英, 丁红萍, 缪小红 ( 2000). 影响水稻种子贮藏的因素. 福建稻麦科技 18(4), 46-47.
[4]	江良荣, 黄荣裕, 黄育民, 王侯聪, 郑景生 ( 2017). 稻米垩白性状的QTL检测、上位性及环境效应分析. 分子植物育种 15, 1385-1394.
[5]	李茂柏, 王慧, 朴钟泽, 沈国辉, 温广月 ( 2010). 杂草稻人工老化和耐储藏特性的初步研究. 作物杂志 ( 5), 30-33.
[6]	李清华, 郑苹立, 吴方喜, 林玲娜, 王乌齐 ( 2009). 优质耐储藏水稻的初步研究和探讨. 中国农学通报 25(17), 47-51.
[7]	柳武革, 王丰, 刘振荣, 廖亦龙, 李金华 ( 2006). 水稻耐储藏特性研究进展. 生物技术通报 (增刊), 50- 52, 62.
[8]	刘喜, 林秋云, 孙爱玲, 曹鹏辉, 姜一梅, 陈亮明, 江玲, 万建民 ( 2015). 水稻种子耐贮性QTL qSS-9的精细定位. 南京农业大学学报 38, 877-882.
[9]	任德勇, 何光华, 凌英华, 桑贤春, 杨正林, 赵芳明 ( 2010). 基于单片段代换系的水稻穗长QTL加性及其上位性效应. 植物学报 45, 662-669.
[10]	任淦, 彭敏, 唐为江, 徐才国, 邢永忠 ( 2005). 水稻种子衰老相关基因定位. 作物学报 31, 183-187.
[11]	商连光, 高振宇, 钱前 ( 2017). 作物杂种优势遗传基础的研究进展. 植物学报 52, 10-18.
[12]	沈圣泉, 庄杰云, 王淑珍, 杨国花, 夏英武 ( 2005). 水稻种子耐贮藏性QTL主效应和上位性效应分析. 分子植物育种 3, 323-328.
[13]	吴方喜, 朱永生, 谢鸿光, 张建福, 谢华安 ( 2010). 中国水稻微核心种质的耐储藏特性初步研究. 中国粮油学报 25(10), 124-128.
[14]	吴贻开, 陈文杰, 李清华, 李清华, 郑向华 ( 2000). 相对湿度对水稻种子贮藏寿命的影响. 福建农业科技 ( 4), 6-7.
[15]	吴跃进, 卢义宣, 吴敬德, 余增亮, 张瑛, 童继平, 郑乐娅, 佘德红 ( 2004). 耐储藏专用型水稻选育及相关技术研究. 中国稻米 ( 3), 6-7.
[16]	吴跃进, 吴先山, 沈宗海, 张瑛, 吴敬德, 卢义宣, 余增亮 ( 2005). 水稻耐储藏种质创新及相关技术研究. 粮食储藏 34, 17-20.
[17]	许惠滨, 江敏榕, 连玲, 朱永生, 蒋家焕, 谢鸿光, 谢华安, 张建福 ( 2017). 稻谷耐储性研究进展. 福建农业科技 ( 11), 41-44.
[18]	许惠滨, 魏毅东, 连玲, 朱永生, 谢华安, 王宗华, 张建福 ( 2013). 水稻种子人工老化与自然老化的分析比较. 分子植物育种 11, 552-556.
[19]	余丽琴, 熊玉珍, 黎二姝, 饶淑芳 ( 2008). 水稻耐贮藏种质资源的筛选. 江西农业学报 20(4), 17-19.
[20]	曾大力, 钱前, 国广泰史, 滕胜, 藤本宽 ( 2002). 稻谷储藏特性及其与籼粳特性的关系研究. 作物学报 28, 551-554.
[21]	张安鹏, 钱前, 高振宇 ( 2018). 水稻种子活力的研究进展. 中国水稻科学 32, 296-303.
[22]	张文明, 倪安丽, 王昌初 ( 1998). 杂交水稻种子活力的研究. 种子 ( 2), 7-10.
[23]	张瑛, 滕斌, 吴敬德, 吴跃进, 宣红, 朱学桂 ( 2010). 水稻种子高温高湿人工加速老化试验方法研究. 中国粮油学报 25(10), 8-12.
[24]	张玉兰, 汪晓峰, 景新明, 林坚 ( 2005). 水稻种子含水量及其对贮藏寿命的影响. 中国农业科学 38, 1480-1486.
[25]	周玉亮, 刘春保, 潘招远, 谭斌, 曾瑞珍 ( 2016). 水稻种子休眠的QTL定位研究进展. 中国科技论文 11, 2837-2844.
[26]	朱军 ( 1997). 遗传模型分析方法. 北京: 中国农业出版社. pp. 240-292.
[27]	Cai HW, Morishima H ( 2000). Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet 100, 840-846.
[28]	Cheng JP, Wang L, Du WL, Lai YY, Huang X, Wang ZF, Zhang HS ( 2014). Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice. Mol Breeding 34, 501-510.
[29]	Dong XY, Fan SX, Liu J, Wang Q, Li MR, Jiang X, Liu ZY, Yin YC, Wang JY ( 2017). Identification of QTLs for seed storability in rice under natural aging conditions using two RILs with the same parent Shennong 265. J Integr Agr 16, 1084-1092.
[30]	Doyle JJ, Doyle JL ( 1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19, 11-15.
[31]	Gao YM, Zhu J ( 2007). Mapping QTLs with digenic epistasis under multiple environments and predicting heterosis ba- sed on QTL effects. Theor Appl Genet 115, 325-333.
[32]	Gu XY, Kianian SF, Foley ME ( 2004). Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics 166, 1503-1516.
[33]	Guo LB, Zhu LH, Xu YB, Zeng DL, Wu P, Qian Q ( 2004). QTL analysis of seed dormancy in rice (Oryza sativa L.). Euphytica 140, 155-162.
[34]	Hang NT, Lin QY, Liu LL, Liu X, Liu SJ, Wang WY, Li LF, He NQ, Liu Z, Jiang L, Wan JM ( 2015). Mapping QTLs related to rice seed storability under natural and artificial aging storage conditions. Euphytica 203, 673-681.
[35]	Jiang WZ, Lee J, Jin TM, Qiao YL, Piao RH, Jang SM, Woo MO, Kwon SW, Liu XH, Pan HY, Du XL, Koh HJ ( 2011). Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice. Mol Cells 31, 385-392.
[36]	Jing W, Jiang L, Zhang WW, Zhai HQ, Wan JM ( 2008). Mapping QTL for seed dormancy in weedy rice. Acta Agron Sin 34, 737-742.
[37]	Li CS, Shao GS, Wang L, Wang ZF, Mao YJ, Wang XQ, Zhang XH, Liu ST, Zhang HS ( 2017). QTL Identification and fine mapping for seed storability in rice (Oryza sativa L.). Euphytica 213, 127.
[38]	Li LF, Lin QY, Liu SJ, Liu X, Wang WY, Hang NT, Liu F, Zhao ZG, Jiang L, Wan JM ( 2012). Identification of quantitative trait loci for seed storability in rice (Oryza sativa L.). Plant Breed 131, 739-743.
[39]	Lu BY, Xie K, Yang CY, Wang SF, Liu X, Zhang L, Jiang L, Wan JM ( 2011). Mapping two major effect grain dormancy QTL in rice. Mol Breeding 28, 453-462.
[40]	McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T ( 1997). Report on QTL nomenclature. Rice Genet Newsl 14, 11-13.
[41]	Miura K, Lin Y, Yano M, Nagamine T ( 2002). Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104, 981-986.
[42]	Sasaki K, Fukuta K, Sato T ( 2005). Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage. Plant Breed 124, 361-366.
[43]	Shigemune A, Miura K, Sasahara H, Goto A, Yoshida T ( 2008). Role of maternal tissues in qLG-9 control of seed longevity in rice( Oryza sativa L.). Breed Sci 58, 1-5.
[44]	Wan JM, Cao YJ, Wang CM, Ikehashi H ( 2005). Quantitative trait loci associated with seed dormancy in rice. Crop Sci 45, 712-716.
[45]	Wang JK, Li HH, Zhang LY ( 2014). QTL ICI Mapping V4.0 [2014]. .
[46]	Xie K, Jiang L, Lu BY, Yang CY, Li LF, Liu X, Zhang L, Zhao ZG, Wan JM ( 2011). Identification of QTLs for seed dormancy in rice (Oryza sativa L.). Plant Breed 130, 328-332.
[47]	Xue Y, Zhang SQ, Yao QH, Peng RH, Xiong AS, Li X, Zhu WM, Zhu YY, Zha DS ( 2008). Identification of quantitative trait loci for seed storability in rice (Oryza sativa L.). Euphytica 164, 739-744.
[48]	Zeng DL, Guo LB, Xu YB, Yasukumi K, Zhu LH, Qian Q ( 2006). QTL analysis of seed storability in rice. Plant Breed 125, 57-60.
[49]	Zhang ZH, Yu SB, Yu T, Huang Z, Zhu YG ( 2005). Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.). Field Crop Res 91, 161-170.
[50]	Zhuang JY, Fan YY, Rao ZM, Wu JL, Xia YW, Zheng KL ( 2002). Analysis on additive effects and additive- by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice. Theor Appl Genet 105, 1137-1145.

Years	Rainy days	Max temperature (°C)	Days of max temperature (>30°C)	Max mean temperature (°C)	Mean min temperature (°C)	Mean temperature (°C)
2016	192	38	101	22.68	16.10	19.39
2017	184	39	97	23.03	16.10	19.57
2018 (1-9 months)	130	38	119	25.34	17.71	21.53

Years	Rainy days	Max temperature (°C)	Days of max temperature (>30°C)	Max mean temperature (°C)	Mean min temperature (°C)	Mean temperature (°C)
2016	192	38	101	22.68	16.10	19.39
2017	184	39	97	23.03	16.10	19.57
2018 (1-9 months)	130	38	119	25.34	17.71	21.53

Trait	Environment (Year)	Parents		RILs population
Trait	Environment (Year)	LD5	ZYZ8	Means±SD	Range	Skewness	Kurtosis
GR (%)	1	63.97±6.10	95.95±4.51**	56.34±26.89	0.00-100.00	-0.30	-0.88
	2	43.19±4.30	59.79±2.20**	32.92±29.32	0.00-96.55	0.49	-1.04
	3	0.00±0.00	56.12±2.05**	6.89±16.80	0.00-87.68	2.92	3.36
Dynamic GR	1-2	20.78±5.20	36.16±2.75**	23.42±29.59	-5.70-97.79	-0.03	0.01
	2-3	43.19±5.63	3.67±3.50**	26.02±28.28	-2.9-96.55	0.64	-0.45

Trait	Environment (Year)	Parents		RILs population
Trait	Environment (Year)	LD5	ZYZ8	Means±SD	Range	Skewness	Kurtosis
GR (%)	1	63.97±6.10	95.95±4.51**	56.34±26.89	0.00-100.00	-0.30	-0.88
	2	43.19±4.30	59.79±2.20**	32.92±29.32	0.00-96.55	0.49	-1.04
	3	0.00±0.00	56.12±2.05**	6.89±16.80	0.00-87.68	2.92	3.36
Dynamic GR	1-2	20.78±5.20	36.16±2.75**	23.42±29.59	-5.70-97.79	-0.03	0.01
	2-3	43.19±5.63	3.67±3.50**	26.02±28.28	-2.9-96.55	0.64	-0.45

Traits	Environment (Year)	1	2	3
GR	1	1.000
	2	0.448**	1.000
	3	0.166*	0.347**	1.000