Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Li, Xiukun; Wu, Lian; Wang, Jiahong; Sun, Jian; Xiu-hong, Xia; Geng, Xin; Wang, Xuhong; Xu, Zhenbo; Xu, Quan

doi:10.1186/s12915-018-0572-x

Cited by 57 publications

(42 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Although both C-terminal and N-terminal regions is thought to be involved in protein interaction, the molecular mechanisms of the observed selfinhibition of GS3 and DEP1 remain elusive [19,30]. As DEP1 plays a crucial role in the understanding of G protein in rice and in rice breeding, a number of studies employing CRISPR/Cas9 technology have been conducted to verified the function of DEP1 [22,31,[38][39][40][41]. The DEP1 CRISPR/Cas9 gene-edited plants with an eliminated C-terminal exhibited an increase in grain number per panicle, reductions in plant height, panicle length, and grain length, and an erect panicle architecture, whereas the plants that had lost both the Gγ and cys-rich domains showed reductions in setting rate and grain number per panicle.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

Cui

Jiang²,

et al. 2020

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

Background: The heterotrimeric G protein complex, consisting of Gα, Gβ, and Gγ subunits, are conserved signal transduction mechanism in eukaryotes. Recent molecular researches had demonstrated that G protein signaling participates in the regulation of yield related traits. However, the effects of G protein genes on yield components and stress tolerance are not well characterized. Results: In this study, we generated heterotrimeric G protein mutants in rice using CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology. The effects of heterotrimeric G proteins on the regulation of yield components and stress tolerance were investigated. The mutants of gs3 and dep1 generated preferable agronomic traits compared to the wild-type, whereas the mutants of rga1 showed an extreme dwarf phenotype, which led to a dramatic decrease in grain production. The mutants showed improved stress tolerance, especially under salinity treatment. We found four putative extra-large G proteins (PXLG)1-4 that also participate in the regulation of yield components and stress tolerance. A yeast two hybrid showed that the RGB1 might interact with PXLG2 but not with PXLG1, PXLG3 or PXLG4. Conclusion: These findings will not only improve our understanding of the repertoire of heterotrimeric G proteins in rice but also contribute to the application of heterotrimeric G proteins in rice breeding.

show abstract

Section: Discussionmentioning

confidence: 99%

“…The plot was 5.4 m 2 and contained 120 plants with 30 cm × 15 cm intervals. The cultivation method and field management were as described previously [38]. We harvested the aboveground parts of 24 plants for each transgenic line at the mature stage (35 days after the full heading stage).…”

Section: Field Experimentsmentioning

confidence: 99%

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

Cui

Jiang²,

et al. 2020

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

show abstract

“…The percentage of phenotypic variance calculation explained by each QTL was obtained according to the population variance within the mapping population. The details of the QTL analysis were described in our previous studies [21].…”

Section: Dna Extraction and Qtl Analysismentioning

confidence: 99%

Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci

Zhu

Cui

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica, and hybrid rice is the predominant form of indica rice in China. However, the molecular mechanism underlying heterosis in japonica remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF 1 lines to uncover the heterosis-related loci for rice yield increase under a japonica genetic background. The BIL population was derived from an admixture variety Habataki and japonica variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to japonica. The results showed that heterosis in F 1 mainly involved grain number per panicle. The BILF 1 s showed an increase in grain number per panicle but a decrease in plant height compared with the BILs. Genetic analysis then identified eight QTLs for heterosis in the BILF 1 s; four QTLs were detected exclusively in the BILF 1 population only, presenting a mode of dominance or super-dominance in the heterozygotes. An additional four loci overlapped with QTLs detected in the BIL population, and we found that Grains Height Date 7 (Ghd7) was correlated in days to heading in both BILs and BILF 1 s. The admixture genetic background of Habataki was also determined by subspecies-specific single nucleotide polymorphisms (SNPs). This investigation highlights the importance of high-throughput sequencing to elucidate the molecular mechanism of heterosis and provides useful germplasms for the application of heterosis in japonica rice production.

show abstract

“…Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region, and indica varieties were planted in low latitudes in southern China (Min et al, 2011;Wang et al, 2015). Over the past decades, many elite japonica varieties have been bred for mid latitudes in China.…”

Section: Introductionmentioning

confidence: 99%

In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods

Liu

Lin

et al. 2020

Front. Plant Sci.

View full text Add to dashboard Cite

Japonica rice has become increasingly popular in China owing to its superior grain quality. Over the past decades, "indica to japonica" projects have been proposed to promote cultivation of japonica rice in low latitudes in China. Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region. The key obstacle for introducing elite mid-latitude japonica varieties to low latitudes is the severe shortening of growth period of the japonica varieties due to their sensitivity to low-latitude short photoperiod and high temperature. Here we report development of new japonica rice with prolonged basic vegetative growth (BVG) periods for low latitudes by targeted editing the Early heading date 1 (Ehd1) gene. Using CRISPR/Cas9 system, we generated both frame-shift and/or in-frame deletion mutants in four japonica varieties, Nipponbare, Longdao16, Longdao24, and Xiushui134. When planting at low-latitude stations, the frame-shift homozygous lines exhibited significantly longer BVG periods compared with wild-types. Interestingly, we observed that minor deletion of the first few residues within the receiver domain could quantitatively impair the function of Ehd1 on activation of Hd3a and RFT1, resulting in an intermediatelong BVG period phenotype in the homozygous in-frame deletion ehd1 lines. Field investigation further showed that, both the in-frame and frame-shift lines exhibited significantly improved yield potential compared with wild-types. Our study demonstrates an effective approach to rapid breeding of elite japonica varieties with intermediate-long and long BVG periods for flexible cropping systems in diverse areas or under different seasons in southern China, and other low-latitude regions.

show abstract

Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Cited by 57 publications

References 63 publications

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci

In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods

Contact Info

Product

Resources

About