Background

Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta.

Results

An introgression line ‘IL188’ has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F₂ and F_2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F₂ and F_2:3 populations, and explained 15.09–16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F_2:3 and four F_2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~ 261 kb region between Indel marker Y7–12 and SSR marker Y7–38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume’s epidermal cells showed that the cell length and width of NIL-qGL7^IL188 was higher than NIL-qGL7^Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion.

Conclusions

In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~ 261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.

中文翻译：

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使用来自水稻和水稻之间杂交的基因渗入系验证谷物大小和重量的 QTL

背景

粒重和粒重是决定水稻产量和品质的重要目标性状。野生稻种拥有大量的优良基因，可以作为水稻遗传改良的重要资源。在这项研究中，我们使用来自水稻和水稻杂交的基因渗入系鉴定并验证了 7 号染色体上影响谷物大小和重量的新 QTL 。

结果

已经从野生物种Oryza minuta (2n = 48, BBCC, W303) 进入O. sativa japonica Nipponbare实现了基因渗入系 'IL188' 。来自 IL188 和日本晴杂交的 F ₂和 F _2:3群体被用于定位五个晶粒尺寸性状的 QTL，包括籽粒长度 (GL)、籽粒宽度 (GW)、籽粒长宽比 (LWR)、粒厚（GT）和千粒重（TGW）。在1、2、3、6、7和8号染色体上共鉴定出5个谷物性状的12个QTL。在F ₂和F _2:3中稳定检测到控制7号染色体上GL的QTL- qGL7种群，并解释了 15.09-16.30% 的表型方差。为了验证qGL7的效果，通过自交四个 F _2:3和四个 F _2:4植物开发了八个残留杂合系 (RHL) 种群，这些植物具有针对目标区域的不同杂合片段。通过在目标区间进一步开发 SSR 和 Indel 标记，qGL7被划定在 Indel 标记 Y7-12 和 SSR 标记 Y7-38 之间的~261 kb 区域，这也显示出对粒宽和千粒重的显着影响。与日本晴的参考基因组相比，三个推定基因LOC_Os07g36830、LOC_Os07g36900和LOC_Os07g36910编码包含 F-box 域的蛋白质可能是qGL7的候选基因。颖片表皮细胞的扫描电镜分析表明，NIL- qGL7 ^IL188的细胞长度和宽度高于 NIL- qGL7 ^Nip，表明qGL7通过调节细胞扩张来增加晶粒大小和重量。

结论

在这项研究中，我们使用来自水稻和水稻杂交的基因渗入系检测到 12 个调节谷物大小和重量的 QTL 。在这些基因座中，我们确认了qGL7并将其定界为 ~ 261 kb 区域。三个假定的基因，LOC_Os07g36830、LOC_Os07g36900和LOC_Os07g36910编码含有 F-box 结构域的蛋白质，可能是qGL7的候选基因。这些结果为基于图谱的qGL7基因克隆提供了基础，并为水稻籽粒质量改进中的标记辅助选择提供了有用的信息。