中国农业科学 ›› 2019, Vol. 52 ›› Issue (3): 385-398.doi: 10.3864/j.issn.0578-1752.2019.03.001
• 作物遗传育种·种质资源·分子遗传学 • 下一篇
孙凯,李冬秀,杨靖,董骥驰,严贤诚,罗立新,刘永柱,肖武名,王慧,陈志强,郭涛
收稿日期:
2018-09-18
接受日期:
2018-11-12
出版日期:
2019-02-01
发布日期:
2019-02-14
通讯作者:
郭涛,E-mail:guo.tao@vip.163.com。陈志强,E-mail:zqchen@scau.edu.cn
作者简介:
孙凯,E-mail:m15018435726_2@163.com
基金资助:
SUN Kai,LI DongXiu,YANG Jing,DONG JiChi,YAN XianCheng,LUO LiXin,LIU YongZhu,XIAO WuMing,WANG Hui,CHEN ZhiQiang,GUO Tao
Received:
2018-09-18
Accepted:
2018-11-12
Online:
2019-02-01
Published:
2019-02-14
摘要:
背景 耐淹成苗率低是限制直播稻产量的重要因素,挖掘高种子活力、低氧萌发能力强的水稻材料是提高耐淹成苗率的关键,但控制耐淹成苗率的遗传位点的挖掘仍然比较有限。目的 利用来源广泛的自然种质,分析影响耐淹成苗率的关键表型性状,挖掘相关的遗传位点和候选基因,为直播稻耐淹成苗机理研究提供一定的理论和材料基础。方法 以200份来源广泛的水稻种质为材料,在有氧环境下进行发芽试验,测量种子发芽率、发芽指数和活力指数;在低氧条件下测量芽鞘长和芽鞘直径;进行耐淹成苗试验,水深10 cm,20 d后测量耐淹成苗率。分析各性状间的相关性,挖掘影响耐淹成苗率的关键性状;利用简化基因组测序对以上6个表型进行全基因组关联分析,鉴定与性状显著关联的SNP位点,并在关联区间内筛选候选基因;对02428和YZX 2份材料进行有氧、无氧以及氧气含量转换条件下的转录组检测,结合全基因组关联分析结果,分析候选基因的表达模式差异。结果 种子活力、芽鞘表型和耐淹成苗率在200份材料间存在广泛的遗传变异,其中,芽鞘长和活力指数的变异系数最大;相关分析结果表明,芽鞘长、活力指数与耐淹成苗率呈极显著正相关;通过全基因组关联分析,共鉴定出8个与活力指数显著关联的位点,15个与芽鞘长显著关联的位点;结合基因组注释,在关联区间筛选出6个与活力指数相关的候选基因,7个与芽鞘长度相关的候选基因;进一步比较13个基因在有氧、无氧及氧气转换条件下的表达模式以及表达量的变化,发现Os02g0657000、Os03g0592500、Os08g0380100表达量变化显著,表现出对氧气处理的敏感性。结论 种子活力、芽鞘长与耐淹成苗率密切相关,可作为筛选高耐淹成苗水稻材料的重要性状。全基因组关联分析、转录组分析与基因表达模式比较的联合应用可提高候选基因的筛选效率。水稻耐淹成苗过程可能受到与逆境胁迫、光合作用相关基因的调控。
孙凯, 李冬秀, 杨靖, 董骥驰, 严贤诚, 罗立新, 刘永柱, 肖武名, 王慧, 陈志强, 郭涛. 水稻耐淹成苗率相关性状全基因组的关联分析[J]. 中国农业科学, 2019, 52(3): 385-398.
SUN Kai, LI DongXiu, YANG Jing, DONG JiChi, YAN XianCheng, LUO LiXin, LIU YongZhu, XIAO WuMing, WANG Hui, CHEN ZhiQiang, GUO Tao. Genome-Wide Association Analysis for Rice Submergence Seedling Rate[J]. Scientia Agricultura Sinica, 2019, 52(3): 385-398.
表1
表型性状"
性状 Trait | 极小值 Min | 极大值 Max | 均值 Average | 标准误 Standard error | 标准差 Standard deviation | 变异系数 Coefficient of variation |
---|---|---|---|---|---|---|
发芽率 Germination rate (%) | 64.9515 | 100.0000 | 95.8427 | 0.3259 | 4.9420 | 5.1564 |
发芽指数 Germination index | 32.6747 | 90.3761 | 59.6827 | 0.6815 | 10.3348 | 17.3162 |
活力指数 Vitality index | 0.1376 | 0.9656 | 0.3345 | 0.0071 | 0.1079 | 32.2571 |
胚芽鞘长 Coleoptile length (cm) | 0.9640 | 3.4622 | 2.3019 | 0.0302 | 0.4577 | 19.8836 |
胚芽鞘直径 Coleoptile diameter (mm) | 0.4544 | 0.6576 | 0.5287 | 0.0026 | 0.0387 | 7.3198 |
成苗率 Seedling rate (%) | 11.1111 | 97.7788 | 61.5295 | 1.3074 | 19.8212 | 32.2141 |
表2
表型相关性分析"
性状 Trait | 成苗率 Seedling rate | 发芽率 Germination rate | 发芽指数 Germination index | 活力指数 Vitality index | 胚芽鞘长 Coleoptile length | 胚芽鞘直径 Coleoptile diameter |
---|---|---|---|---|---|---|
成苗率 Seedling rate | 1 | |||||
发芽率 Germination rate | 0.254** | 1 | ||||
发芽指数 Germination index | 0.229** | 0.422** | 1 | |||
活力指数Vitality index | 0.224** | 0.129 | 0.518** | 1 | ||
胚芽鞘长 Coleoptile length | 0.271** | 0.129* | 0.287** | 0.305** | 1 | |
胚芽鞘直径 Coleoptile diameter | -0.078 | -0.382** | -0.226** | 0.022 | 0.137* | 1 |
表3
活力指数关联位点"
染色体 Chr. | SNP位置 Position (bp) | 等位基因 Allele | 峰值 Peak value | 已报道的位点 Known loci |
---|---|---|---|---|
1 | 13783629 | C/T | 6.322302731 | |
2 | 26540479 | A/G | 6.142571185 | [18-19] |
5 | 3878312 | A/G | 6.384993065 | |
6 | 5542656 | C/T | 8.912458149 | [20] |
10 | 13589547 | C/T | 6.960402683 | [20-21] |
11 | 4608768 | A/G | 7.710957603 | |
11 | 26538371 | G/T | 6.863393569 | |
12 | 23449435 | T/C | 6.103889317 | [22-23] |
表4
活力指数关联位点候选基因"
SNP位置 SNP position | 基因编号 Gene ID | 基因注释 Gene annotation |
---|---|---|
Chr.01_13783629 | Os01g0347500 | 木瓜蛋白酶样半胱氨酸蛋白酶 Papain-like cysteine proteinase |
Chr.02_26540479 | Os02g0657000 | 含AP2结构域的蛋白质 AP2 domain-containing protein |
Chr.02_26540479 | Os02g0658200 | 锌指,含有PHD型结构域的蛋白质 Zinc finger, PHD-type domain containing protein |
Chr.02_26540479 | Os02g0658400 | Remorin,含有C末端结构域的蛋白质 Remorin, C-terminal domain containing protein |
Chr.11_26538371 | Os11g0660300 | 热激蛋白DnaJ,含有N-末端结构域的蛋白质 Heat shock protein DnaJ, N-terminal domain containing protein |
Chr.11_26538371 | Os11g0661200 | 糖苷水解酶 Glycoside hydrolasen |
表5
胚芽鞘长关联位点"
染色体 Chr. | SNP位置 Position (bp) | 等位基因 Allele | 峰值 Peak value | 已报道的位点 Known loci |
---|---|---|---|---|
3 | 22007803 | C/T | 5.023909483 | |
4 | 6615471 | A/G | 4.342639196 | |
4 | 23562335 | T/C | 4.028691488 | |
5 | 15450007 | G/A | 4.777759954 | [24] |
6 | 757734 | A/G | 4.284055624 | |
6 | 9693092 | A/G | 4.340712509 | |
6 | 21932341 | T/C | 4.165186256 | [25-26] |
6 | 29822164 | T/A | 4.48136579 | [27-28] |
8 | 5689664 | C/T | 4.675971197 | [29] |
8 | 18019426 | T/C | 4.364278864 | |
10 | 3160014 | G/A | 4.652868342 | |
10 | 7504391 | T/C | 4.286580613 | |
10 | 17384859 | G/C | 4.84143398 | |
11 | 10896433 | T/C | 4.076205999 | |
11 | 18620615 | C/A | 4.169961251 |
表6
胚芽鞘长关联位点候选基因"
SNP位置 SNP Position | 基因编号 Gene ID | 基因注释 Gene annotation |
---|---|---|
Chr.03_22007803 | Os03g0595600 | 谷胱甘肽转移酶 Glutathione transferase |
Chr.03_22007803 | Os03g0592500 | 叶绿素a-b结合蛋白 Chlorophyll a-b binding protein |
Chr.06_29822164 | Os06g0704300 | 锌指CCCH结构域的蛋白质 Zinc finger CCCH domain-containing protein |
Chr.08_15689664 | Os08g0198200 | 天冬氨酸蛋白酶CDR1 Aspartic proteinase CDR1 |
Chr.08_18019270 | Os08g0380100 | 含有BURP结构域的蛋白质 BURP domain-containing protein |
Chr.10_17384859 | Os10g0466500 | 锌指蛋白CONSTANS-LIKE 4 Zinc finger protein CONSTANS-LIKE 4 |
Chr.11_10896433 | Os11g0293900 | 植物含UBX结构域的蛋白质 Plant UBX domain-containing protein |
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