Dynamic Quantitative Trait Locus Analysis of Seed Vigor at Three Maturity Stages in Rice

Liu, Liangfeng; Lai, Yanyan; Jiaan, Cheng; Wang, Ling; Du, Wenli; Wang, Zhoufei; Zhang, Hongsheng

doi:10.1371/journal.pone.0115732

Cited by 33 publications

(24 citation statements)

References 49 publications

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“…However, the argininosuccinate synthase and pyruvate phosphate dikinase protein were first time found to be involved in seed germination under salt stress. Six genes encoding the proteins identified here are near the regions of QTLs for seed dormancy, seed reserve utilization, seed imbibition and seed germination in our previous studies (Wang et al, 2011, 2014; Cheng et al, 2013; Liu et al, 2014). It indicates that these genes might be important for seed germination.…”

Section: Discussionmentioning

confidence: 51%

“…The proteins identified in this study are shown on the left (red), and the previously mapped QTLs are shown on the right (blue) (Wang et al, 2011, 2014; Cheng et al, 2013; Liu et al, 2014). …”

Section: Resultsmentioning

confidence: 96%

“…The genome regions of QTLs for seed germination in Jiucaiqing (Wang et al, 2011, 2014; Cheng et al, 2013; Liu et al, 2014) and genes encoding the identified proteins here were compared (Figure 5). Four genes, BPM, GLU2.3, GLU2.2 , and CDP3.2 , were near the regions of three QTLs for seed dormancy in Jiucaiqing.…”

Section: Resultsmentioning

confidence: 99%

“…Previously, we have identified one salt-tolerant japonica landrace Jiucaiqing from Taihu Lake valley in Jiangsu Province of China (Wang et al, 2011, 2012a,b). By using bi-parental population, we have identified several quantitative trait locus (QTLs) in Jiucaiqing for seed dormancy (Wang et al, 2014), seed reserve utilization (Cheng et al, 2013), seed vigor (Liu et al, 2014), and salt tolerance at seed germination (Wang et al, 2011) and seedling stages (Wang et al, 2012a,b). Recently, we found that the proteins associated with seed imbibition in distilled water could be categorized as carbohydrate and protein biosynthesis and metabolism-related, signaling-related, storage, and stress-related proteins in Jiucaiqing (Cheng et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice

Chen

et al. 2017

Front. Plant Sci.

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Enhancement of salinity tolerance during seed germination is very important for direct seeding in rice. In this study, the salt-tolerant japonica landrace Jiucaiqing was used to determine the regulators that are involved in seed imbibition under salt stress. Briefly, the comparative proteomic analysis was conducted between dry (0 h) and imbibed (24 h) seeds with 150 mM NaCl. Under salt stress, the uptake of water increased rapidly before 24 h imbibition (Phase I), followed by a plateau of seed imbibition from 24 to 96 h imbibition (Phase II). We identified 14 proteins involved in seed imbibition, in which the majority of these proteins were involved in energy supply and storage protein. The early imbibition process was mediated by protein catabolism; the most of proteins were down-regulated after 24 h imbibition. Eleven genes in salt stress treated seeds were expressed early during the seed imbibition in comparison to control seeds. By comparison, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (BPM), glutelin (GLU2.2 and GLU2.3), glucose-1-phosphate adenylyltransferase large subunit (GAS8), and cupin domain containing protein (CDP3.1 and CDP3.2) were near the regions of quantitative trait loci (QTLs) for seed dormancy, seed reserve utilization, and seed germination in Jiucaiqing. In particular, CDP3.1 was co-located in the region of qIR-3 for imbibition rate, and qGP-3 for germination percentage. The role of CDP3.1 was verified in enhancing seed germination under salt stress using T-DNA mutant. The identified proteins might be applicable for the improvement of seed germination under salt stress in rice.

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Section: Discussionmentioning

confidence: 51%

Section: Resultsmentioning

confidence: 96%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice

Chen

et al. 2017

Front. Plant Sci.

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“…SLAF markers were ordered in terms of high map strategy and smoothing strategy. Genotyping errors in the linkage groups were corrected [31,32]. The imputation of missing genotypes was performed using the K-nearest neighbour algorithm based on the two parents and the BC 4 F 3 population [33].…”

Section: Linkage Map Constructionmentioning

confidence: 99%

Construction of High-Density Genetic Map and Identification of QTLs Associated with Seed Vigor after Exposure to Artificial Aging Conditions in Sweet Corn Using SLAF-seq

Feng

Zhu

et al. 2019

Genes

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Seed vigor is a key factor that determines the quality of seeds, which is of great significance for agricultural production, with the potential to promote growth and productivity. However, the underlying molecular mechanisms and genetic basis for seed vigor remain unknown. High-density genetic linkage mapping is an effective method for genomic study and quantitative trait loci (QTL) mapping. In this study, a high-density genetic map was constructed from a 148 BC 4 F 3 population cross between 'M03' and 'M08' strains based on specific-locus amplified fragment (SLAF) sequencing. The constructed high-density genetic linkage map (HDGM) included 3876 SNP markers on ten chromosomes covering 2413.25 cM in length, with a mean distance between markers of 0.62 cM. QTL analysis was performed on four sweet corn germination traits that are related to seed vigor under artificial aging conditions. A total of 18 QTLs were identified in two seasons. Interestingly, a stable QTL was detected in two seasons on chromosome 10-termed qGR10-within an interval of 1.37 Mb. Within this interval, combined with gene annotation, we found four candidate genes (GRMZM2G074309, GRMZM2G117319, GRMZM2G465812, and GRMZM2G343519) which may be related to seed vigor after artificial aging.

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

Dwivedi¹,

Spillane

Lopez

et al. 2021

Crop Science

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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.

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Dynamic Quantitative Trait Locus Analysis of Seed Vigor at Three Maturity Stages in Rice

Cited by 33 publications

References 49 publications

Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice

Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice

Construction of High-Density Genetic Map and Identification of QTLs Associated with Seed Vigor after Exposure to Artificial Aging Conditions in Sweet Corn Using SLAF-seq

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

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