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作物学报 ›› 2018, Vol. 44 ›› Issue (6): 938-946.doi: 10.3724/SP.J.1006.2018.00938

• 研究简报 • 上一篇    

基于高密度Bin图谱的水稻抽穗期QTL定位

董骥驰,杨靖,郭涛,陈立凯,陈志强(),王慧()   

  1. 华南农业大学 / 国家植物航天育种工程技术研究中心, 广东广州 510642
  • 收稿日期:2017-12-14 接受日期:2018-03-25 出版日期:2018-06-12 网络出版日期:2018-04-16
  • 通讯作者: 陈志强,王慧
  • 基金资助:
    本研究由国家现代农业产业技术体系建设专项(CARS-01-12);国家重点研发计划项目(2016YFD0102102);广东省应用型研发项目资助(2015B020231011)

QTL Mapping for Heading Date in Rice Using High-density Bin Map

Ji-Chi DONG,Jing YANG,Tao GUO,Li-Kai CHEN,Zhi-Qiang CHEN(),Hui WANG()   

  1. National Engineering Research Centre of Plant Space Breeding / South China Agricultural University, Guangzhou 510642, Guangdong, China
  • Received:2017-12-14 Accepted:2018-03-25 Published:2018-06-12 Published online:2018-04-16
  • Contact: Zhi-Qiang CHEN,Hui WANG
  • Supported by:
    This study was supported by the China Agriculture Research System(CARS-01-12);the National Key Research and Development Program of China(2016YFD0102102);the Research and Development Program for Application in Guangdong Province(2015B020231011)

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摘要：

以粳稻品种02428和籼稻品种玉针香进行杂交, 按单粒传法连续自交10代, 得到包含192个株系的重组自交系(RIL)作图群体。通过对两亲本重测序及RIL群体简化基因组测序, 构建了包含2711个Bin标记的高密度遗传图谱。该图谱各染色体标记数在162~311个之间, 标记间平均物理距离为137.68 kb。将亲本及192个株系分别于4个环境下采用随机区组种植, 并记录抽穗期。使用WinQTL Cartographer 2.5软件的CIM分析方法, 进行抽穗期相关QTL检测及定位。在4个环境下定位到影响抽穗期的QTL共14个, 分布于第1、第2、第3、第7、第8、第9和第10染色体。其中, qHD2.2和qHD10.2能在3个环境中被重复检测到, 表型贡献率分别为5.14%~11.15%和5.35%~16.97%, 分别能缩短抽穗期1.66 d和1.56 d, 具有聚合育种的应用价值。通过物理位置比对, 14个QTL中有11个与前人定位在相同或邻近区域, qHD1.1、qHD2.2和qHD9.1尚未见报道。经对qHD2.2详细分析, 在其染色体区间内找到3个与抽穗期相关的注释基因LOC_Os02g46450、LOC_Os02g46710和LOC_Os02g46940, 其中LOC_Os02g46450已被克隆。测序分析发现, 这3个基因在两亲本间都存在差异, 可作为候选基因。

关键词: 水稻, 抽穗期, Bin图谱, QTL定位

Abstract:

A recombination inbred lines (RIL) population including 192 lines derived from an inter-subspecific cross between indica rice ‘Yuzhenxiang’ and japonica rice ‘02428’ was used in the experiment. The two parent varieties and RIL population were separately sequenced by Whole Genome Sequencing (WGS) and Genotyping-By-Sequencing (GBS) to construct a genetic linkage map with 2711 recombination Bin markers. The number of markers on 12 chromosomes ranged from 162 to 311, and the average physical distance between two markers was 137.68 kb. The WinQTL Cartographer 2.5 was used to analysis QTLs associated with heading date in four different environments. A total of 14 QTLs associated with heading date were detected on chromosomes 1, 2, 3, 7, 8, 9, and 10. Among them, qHD2.2 and qHD10.2, which explained 5.14%-11.15% and 5.35%-16.97% of the total phenotypic variation for heading date separately, could be detected in three environments and shorting heading date about 1.66 days and 1.56 days on average. The two QTLs could inherit stablely, having a good potential to be applied in QTL pyramiding. After comparing the physical positions of these QTLs with those previously reported, we found 11 QTLs were located in the same or near position, among them qHD1.1, qHD2.2, and qHD9.1 were newly reported. Furthermore, we found one cloned gene LOC_Os02g46450 and two annotated genes LOC_Os02g46710 and LOC_Os02g46940 in the genomic region of qHD2.2, might be related to heading date. DNA sequence comparison between YZX and 02428 revealed that all the three genes could be candidate genes.

Key words: rice, heading date, Bin map, QTL mapping

图1

遗传标记在染色体上的分布及QTL位置 每条染色体上的黑色线条代表Bin标记所在位置; 红色字体为已克隆QTL; 蓝色字体为新发现的QTL。"

表1

02428与玉针香抽穗期天数比较"

环境
Environment		 平均值Average (d) 变异系数CV (%) 差异
Difference
02428 玉针香 Yuzhenxiang 02428 玉针香 Yuzhenxiang
E1 91.36 97.00 1.08 1.57 -5.64**
E2 64.11 69.27 3.25 3.60 -5.16**
E3 89.20 97.03 0.84 0.76 -7.83**
E4 65.00 70.33 3.91 3.75 -5.33**

表2

RIL群体抽穗期性状表现"

环境
Environment		 平均值±标准差
Mean ± SD		 变异范围
Range		 峰度
Kurtosis		 偏度
Skewness
E1 95.64±6.25 81.33-117.83 0.44 0.60
E2 69.15±4.92 53.13-85.40 0.30 0.27
E3 95.29±4.99 81.00-110.30 0.43 0.11
E4 70.54±4.15 61.30-87.50 0.48 0.46

图2

玉针香/02428重组自交系及亲本的抽穗期表型分布特征"

表3

4个环境下检测到的抽穗期QTL"

环境
Environ- ment		 QTL 染色体
Chr.		 位置
Peak position (cM)		 LOD 加性效应1)
Additive effect1)		 贡献率
Variation
explained (%)		 Bin标记区间
Bin marker
interval		 置信区间
Confidence interval
(Mb)
E1 qHD2.2 2 178.2 3.0 -1.5 5.1 mk487-491 28.25-28.65
E1 qHD3.1 3 194.2 2.9 -1.4 4.7 mk813-814 30.55-30.65
E1 qHD3.2 3 205.1 3.2 -1.5 5.2 mk826-831 31.85-32.45
E1 qHD3.3 3 211.2 3.2 -1.5 5.3 mk836-840 33.10-33.55
E1 qHD7.1 7 48.8 4.2 1.7 7.0 mk1618-1620 8.65-8.85
E1 qHD8.1 8 42.4 5.6 2.0 9.5 mk1821-1824 4.20-4.55
E1 qHD8.2 8 49.3 4.3 1.7 7.4 mk1825-1830 4.65-5.15
E1 qHD10.1 10 56.7 3.5 -1.6 6.7 mk2244-2247 16.35-16.65
E1 qHD10.2 10 64.8 3.2 -1.5 5.4 mk2248-2253 16.75-17.25
E2 qHD2.1 2 173.6 3.2 -1.3 5.8 mk481-488 27.60-28.35
E2 qHD2.2 2 179.7 5.0 -1.6 9.5 mk489-491 28.45-28.65
E2 qHD7.2 7 118.4 3.0 -1.2 5.2 mk1723-1727 22.05-22.55
E2 qHD10.2 10 62.1 4.5 -1.4 8.2 mk2248-2253 16.75-17.25
E2 qHD10.3 10 67.4 4.1 -1.4 7.5 mk2258-2260 17.75-17.95
E3 qHD1.1 1 160.1 2.5 -1.3 4.4 mk185-186 25.95-26.05
E3 qHD2.2 2 175.2 5.9 -1.9 11.1 mk486-491 28.15-28.65
E3 qHD8.1 8 42.4 3.9 2.4 7.4 mk1821-1824 4.20-4.55
E4 qHD3.1 3 197.3 3.4 -1.0 5.6 mk812-818 30.45-31.05
E4 qHD3.2 3 205.1 3.0 -1.0 4.9 mk826-831 31.85-32.45
E4 qHD9.1 9 125.4 2.8 -1.0 4.6 mk2088-2090 16.55-16.75
E4 qHD10.2 10 63.5 9.6 -1.7 17.0 mk2249-2250 16.85-16.95
E4 qHD10.3 10 70.0 7.1 -1.5 13.5 mk2259-2260 17.85-17.95

图3

玉针香与02428之间候选基因的结构和变异 A: LOC_Os02g46450; B: LOC_Os02g46710; C: LOC_Os02g46940。黑色框: 外显子; 灰色部分: 编码序列; 红色箭头: SNP; 带黑点红色箭头: 错义突变; 蓝色箭头: 插入缺失。"

表4

QTL置信区间内注释基因筛选"

QTL 染色体
Chromosome		 置信区间
Confidence interval (Mb)		 抽穗期相关注释(克隆)基因1)
Annotated (cloned) gene1)
qHD1.1 1 25.95-26.05 LOC_Os01g45760
qHD2.1 2 27.60-28.35 OsPIE1 (LOC_Os02g46450)
qHD2.2 2 28.45-28.65 LOC_Os02g46710; LOC_Os02g46940
qHD3.1 3 30.45-31.05 LOC_Os03g53190; LOC_Os03g54160; LOC_Os03g54170
qHD3.2 3 31.85-32.45 LOC_Os03g55990
qHD3.3 3 33.10-33.55 LOC_Os03g58400; LOC_Os03g58530; LOC_Os03g58530
qHD7.1 7 8.65-8.85
qHD7.2 7 22.05-22.55
qHD8.1 8 4.20-4.55 DTH8 (LOC_Os08g07740)
qHD8.2 8 4.65-5.15 LOC_Os08g08210; LOC_Os08g08830
qHD9.1 9 16.55-16.75
qHD10.1 10 16.35-16.65
qHD10.2 10 16.85-16.95 Ehd1 (LOC_Os10g32600)
qHD10.3 10 17.85-17.95
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