Identification of QTL for seed dormancy from weedy rice and its application to elite rice cultivar ‘Ninggeng 4’

Nguyen, Thanhliem; Zhou, Chunlei; TianYu, Zhang; Yu, Jiangfeng; Miao, Ran; Huang, Yunshuai; Zhu, Xingjie; Song, Weihan; Liu, Xi; Mou, Changling; Lan, Jie; Liu, Shijia; Tian, Yunlu; Zhao, Zhigang; Jiang, Ling; Wan, Jianmin

doi:10.1007/s11032-019-1031-2

Cited by 9 publications

(6 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…'Ninggeng 4' is a high yielding japonica cultivar released nationally in China but ultra-susceptible to PHS (85% germination). Nguyen et al (2019) developed near isogenic lines (NILs) containing qSdr7-2 allele from 'LüDao' in 'Ninggeng 4' offspring with strong seed dormancy. NILs were agronomically similar to 'Ninggeng 4' in phenology, panicle architecture and seed characteristics but out yielded significantly (P < 0.01) 'Ninggeng 4'.…”

Section: Genomic Assisted Breeding To Select For Preharvest Sproutingmentioning

confidence: 99%

“…mir156abckl mutations) enhance seed dormancy and suppress preharvest sprouting (PHS) without causing any adverse effect on shoot architecture and seed size, whereas mutations in another MIR156 subfamily (i.e. mri156defghi mutations) modify shoot architecture and increase seed size but have minimal effects on seed dormancy (Miao et al 2019). The mir156abckl mutations enhance seed dormancy by suppressing the GA pathway through upregulation of the gene IPA1, providing an effective route to suppression of PHS without compromising productivity.…”

Section: Seed Dormancy and Germinationmentioning

confidence: 99%

“…The qSdr7-2 NILs with strong seed dormancy are a useful genetic resource in breeding for PHS resistance in rice. Likewise, mutations in miR156 subfamily through CRISPR/Cas9, such as mir156abckl, markedly enhanced seed dormancy and inhibit PHS with negligible effects on shoot architecture and seed size and prolonged seed viability, thereby resulting in an efficient and effective method to inhibit PHS and increase seed longevity without compromising productivity (Miao et al 2019).…”

Section: 2mentioning

confidence: 99%

See 2 more Smart Citations

First the seed: Genomic advances in seed science for improved crop productivity and food security

Dwivedi¹,

Spillane

Lopez

et al. 2021

Crop Science

View full text Add to dashboard Cite

Seeds are valuable sources of carbohydrates, lipids, proteins, fibers, minerals, and vitamins. They provide energy and nutrition to germinating seedlings, food to humans, feed to livestock and feedstocks to industry. High-throughput analyses of gene expression in crops has identified many candidate genes associated with seed dormancy, longevity, germination, and vigor. In this review, we cover the latest research focusing on such key seed traits. Transcriptome analyses of time-courses of seed filling have identified sets of genes expressed at different stages of this process. The potential role of epigenetics (including seed-endosperm imprinted genes) in regulating seed development and chemistry is highlighted herein. We also discuss how advances in genomics and seed biology are facilitating the unravelling of associations between seed traits with genebank accessions and gene sequences, including how functional research can accelerate the discovery of allelic variants. Such knowledge of functional effects relating to gene variants is necessary for more efficient and cost-effective management of genetic resources or for redesigning crops with specific seed characteristics. For instance, genebank curators may assess seed viability by monitoring changes in gene expression of biomarker genes in dry seed samples to decide germplasm regeneration and assess genetic integrity of collections by monitoring changes in This article is protected by copyright. All rights reserved. diversity and allele frequencies between samples of same accession stored in genebanks. We highlight that resistance to preharvest sprouting can be enhanced through genomicsassisted breeding in otherwise nondormant rice and wheat cultivars, while pimt, another valuable marker for seed longevity, may be deployed to enhance seed vigor in crops.

show abstract

Section: Genomic Assisted Breeding To Select For Preharvest Sproutingmentioning

confidence: 99%

Section: Seed Dormancy and Germinationmentioning

confidence: 99%

Section: 2mentioning

confidence: 99%

See 1 more Smart Citation

First the seed: Genomic advances in seed science for improved crop productivity and food security

Dwivedi¹,

Spillane

Lopez

et al. 2021

Crop Science

View full text Add to dashboard Cite

show abstract

“…Loci related to weedy traits were identified through genome-wide selection signature analysis with a focus on known domestication-related genes such as Bh4 , PROG1 , Rc , sh4 (Huang et al 2018 ; Li et al 2017 ; Qiu et al 2017 ). The actual phenotype-genotype studies on weedy traits were relatively few (Nguyen et al 2019 ; Ye et al 2013 ). However, the knowledge on weedy trait genetics would help in a better WR management.…”

Section: Introductionmentioning

confidence: 99%

Explore the genetics of weedy traits using rice 3K database

Lin

et al. 2021

Bot Stud

View full text Add to dashboard Cite

Background Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). Results Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. Conclusions The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

show abstract

“…In rice ( Oryza sativa L.), large variations in seed dormancy are observed between the two cultivated subspecies japonica and indica . More than 150 quantitative trait loci (QTLs) associated with seed dormancy have been identified in various biparental mapping populations (Lin et al 1998 ; Cai and Morishima 2000 ; Wan et al 2006 ; Gu et al 2010 ; Marzougui et al 2012 ; Mizuno et al 2018 ; Nguyen et al 2019 ) ( https://archive.gramene.org/qtl/ ). In addition, several loci affecting seed dormancy have been detected through genome-wide association mapping in rice (Magwa et al 2016 ; Lu et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

Zhang

Yuan

Wang

et al. 2020

Rice

View full text Add to dashboard Cite

Background: Seed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. The genetic and molecular mechanisms underlying seed dormancy in rice remain largely unknown. Results: Quantitative trait loci (QTLs) for seed dormancy were identified in two different mapping populations, a chromosome segment substitution line (CSSL) and backcross inbred line (BIL) population, both derived from the same parents Nipponbare, a japonica cultivar with seed dormancy, and 9311, an indica cultivar lacking seed dormancy. A total of 12 and 27 QTL regions for seed dormancy were detected in the CSSLs and BILs, respectively. Among these regions, four major loci (qSD3.1, qSD3.2, qSD5.2 and qSD11.2) were commonly identified for multiple germination parameters associated with seed dormancy in both populations, with Nipponbare alleles delaying the seed germination percentage and decreasing germination uniformity. Two loci (qSD3.1 and qSD3.2) were individually validated in the near-isogenic lines containing the QTL of interest. The effect of qSD3.2 was further confirmed in a CSSL-derived F 2 population. Furthermore, both qSD3.1 and qSD3.2 were sensitive to abscisic acid and exhibited a significant epistatic interaction to increase seed dormancy. Conclusions: Our results indicate that the integration of the developed CSSLs and BILs with high-density markers can provide a powerful tool for dissecting the genetic basis of seed dormancy in rice. Our findings regarding the major loci and their interactions with several promising candidate genes that are induced by abscisic acid and specifically expressed in the seeds will facilitate further gene discovery and a better understanding of the genetic and molecular mechanisms of seed dormancy for improving seed quality in rice breeding programs.

show abstract

Identification of QTL for seed dormancy from weedy rice and its application to elite rice cultivar ‘Ninggeng 4’

Cited by 9 publications

References 40 publications

First the seed: Genomic advances in seed science for improved crop productivity and food security

First the seed: Genomic advances in seed science for improved crop productivity and food security

Explore the genetics of weedy traits using rice 3K database

Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

Contact Info

Product

Resources

About