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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (6): 938-946.doi: 10.3724/SP.J.1006.2018.00938

• RESEARCH NOTES • Previous Articles    

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 Online:2018-06-12 Published:2018-04-16
  • Contact: Zhi-Qiang CHEN,Hui WANG E-mail:chenlin@scau.edu.cn;wanghui@scau.edu.cn
  • 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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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

Fig. 1

Distribution of genetic markers and QTLs on chromosomes Black lines represent the positions of Bin markers on each linkage group; fonts in red are cloned QTLs; fonts in blue are novel QTLs."

Table 1

Comparison of heading date between 02428 and YZX"

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**

Table 2

Phenotypic performance of RILs for heading date"

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

Fig. 2

Distribution of heading date for YZX/02428 RIL population and parents"

Table 3

QTLs detected for heading date in four environments"

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

Fig. 3

Gene structure and variation of candidate genes between YZX and 02428 A: LOC_Os02g46450; B: LOC_Os02g46710; C: LOC_Os02g46940. Frames with black lines: exon; Grey boxes: protein coding sequence; Red arrow: SNP; Red arrow with a black point: missense mutation; Blue arrow: InDel."

Table 4

Annotated genes in confidence interval of QTLs"

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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