Chin Bull Bot ›› 2019, Vol. 54 ›› Issue (4): 464-473.doi: 10.11983/CBB18188

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

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

Liu Jin1,2,Yao Xiaoyun1,2,Yu Liqin1,Li Hui1,Zhou Huiying1,Wang Jiayu2,*(),Li Maomao1,*()   

  1. 1 Nanchang Sub-center, National Rice Improvement Center/National Engineering Laboratory for Rice (Nanchang)/Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
    2 Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, china
  • Received:2018-09-03 Accepted:2019-02-11 Online:2020-01-08 Published:2019-07-01
  • Contact: Wang Jiayu,Li Maomao E-mail:ricewjy@126.com;Lmm3056@163.com

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

Table 1

Summary of temperature and rainfall conditions from 2016-2018 in Nanchang city"

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

Figure 1

Distribution of germination rates (GR) under different seed dormancy time in the recombinant inbred lines (RILs) population of rice (A)-(C) GR of natural storage condition for 1, 2 and 3 years, respectively; (D), (E) Dynamic GR of natural storage condition for 1-2 and 2-3 years, respectively. GR of the parents (LD5 and ZYZ8) are indicated by black and dotted line arrows, respectively."

Table 2

Distribution of germination rate (GR) after different aging treatments for parents and recombinant inbred lines (RILs) population of rice"

Trait Environment (Year) Parents RILs population
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

Table 3

Correlation coefficients among germination rates (GR) of rice under different natural storage conditions"

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

Figure 2

Location of QTLs detected for seed storability under natural storage conditions in rice on the genetic map of recom- binant inbred lines (RILs)"

Table 4

Putative QTL for seed storability were detected under natural storage conditions in rice"

Trait Locus Position Marker LOD value PVE (%) Additive effect
1 year qSS3 75.5 RM6676-STS3.8 2.53 10.58 -8.77
qSS4 26.1 R4M17-RM5688 2.85 14.49 10.27
qSS6a 121.4 RM5814-RM412 5.28 13.53 -10.27
qSS7a 96.2 RM8261-RM1209 2.85 7.29 -7.27
qSS8a 85.5 R8M33-RM6976 2.79 6.88 -7.04
2 years qSS2a 40.5 RM5897-RM5699 3.86 10.47 9.69
qSS6b 107.4 RM6395-RM5814 2.88 11.27 -10.19
qSS7b 108.2 RM3555-RM1306 2.71 5.78 -7.03
qSS8b 89.5 R8M33-RM6976 3.79 12.12 -10.18
3 years qSS1 102.5 R1M30-RM3240 3.13 9.20 5.78
qSS2b 50.5 RM5699-RM300 3.01 6.46 4.29
qSS7c 64.2 RM1135-RM11 3.21 10.05 5.32
1-2 years qss2 41.5 RM5897-RM5699 2.98 10.13 -9.59
2-3 years qss3 40.5 STS3.3-STS3.4 4.46 25.22 16.95
qss6 107.4 RM6395-RM5814 6.52 32.76 -16.78
qss8 91.5 R8M33-RM6976 2.54 5.60 -6.68
qss12 86 STS12.2-RM1226 2.89 24.42 -14.64

Figure 3

QTL with epistasis effect estimate for seed storability in rice under natural storage conditions"

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