Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq

Yang, Jing; Guo, Zhenhua; Luo, Lixin; Gao, Qiaoli; Xiao, Wuming; Wang, Jiafeng; Wang, Hui; Chen, Zhiqiang; Guo, Tao

doi:10.1016/j.cj.2020.08.010

Cited by 22 publications

(15 citation statements)

References 46 publications

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“…interval of which qAGP1 (Liu et al, 2021). QCL4-2/qCV4-2 and qCV8-2 are in the same physical regions as qSFW-4 and qRD-8, respectively (Yang et al, 2021). The physical area of qCSA4-2 is consistent with that of qCL-4-1; The physical location of qCD12-3 coincides with that of qAG12/qCSA-12-2 (Hsu and Tung, 2015;Yang et al, 2019).…”

Section: Identification Of Ag-associated Qtlsmentioning

confidence: 81%

“…The new generation of sequencing technology can facilitate directly obtaining population single nucleotide polymorphism (SNP) markers for genotyping (Kumar et al, 2012). Previous studies in rice have proved that the improvement of the quality and resolution of high-density genetic maps based on SNP markers has greatly improved the efficiency and accuracy of QTL mapping (Huang et al, 2009;Gao et al, 2013;Wang et al, 2018;Yang et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

Liang

Du²,

Pang³

et al. 2022

Front. Plant Sci.

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The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

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Section: Identification Of Ag-associated Qtlsmentioning

confidence: 81%

Section: Introductionmentioning

confidence: 99%

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

Liang

Du²,

Pang³

et al. 2022

Front. Plant Sci.

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“…Vigorous seeds have high germination rates (GR), or the inverse of the time to radicle emergence of a specific percentage (GR g or 1/t g ), and the values of GR g decline as seeds age and vigor decreases. Recently, GR has informed genetic analyses of seed vigor in small, direct-seeded crops such as Brassica oleracea (Bettey et al 2000) and rice (Guo et al 2019;Yang et al 2021), as well as large-seeded crops such as field pea (Lamichaney, Parihar, et al 2021). Unfortunately, this measure of seed vigor is underutilized as it requires repeated observations of germination percentages at frequent intervals, which is too laborintensive for routine seed testing.…”

Section: Measuring Seed Vigormentioning

confidence: 99%

“…In coordination with genome-wide association studies (GWAS), RILs have helped identify specific candidate seed vigor genes (Guo et al 2019). Differential gene expression analysis paired with QTL mapping provides an additional avenue for identifying candidate vigor genes (Yang et al 2021). Recently, QTLs associated with vigor are also being identified in wild rice varieties and provide additional options for backcrossing seed vigor QTLs into domesticated cultivars for high yielding, high vigor rice (Jin et al 2018).…”

Section: Current Approaches To Improve Seed Vigor Seed Priming/treatingmentioning

confidence: 99%

Seed germination and vigor: ensuring crop sustainability in a changing climate

2022

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In the coming decades, maintaining a steady food supply for the increasing world population will require high-yielding crop plants which can be productive under increasingly variable conditions. Maintaining high yields will require the successful and uniform establishment of plants in the field under altered environmental conditions. Seed vigor, a complex agronomic trait that includes seed longevity, germination speed, seedling growth, and early stress tolerance, determines the duration and success of this establishment period. Elevated temperature during early seed development can decrease seed size, number, and fertility, delay germination and reduce seed vigor in crops such as cereals, legumes, and vegetable crops. Heat stress in mature seeds can reduce seed vigor in crops such as lettuce, oat, and chickpea. Warming trends and increasing temperature variability can increase seed dormancy and reduce germination rates, especially in crops that require lower temperatures for germination and seedling establishment. To improve seed germination speed and success, much research has focused on selecting quality seeds for replanting, priming seeds before sowing, and breeding varieties with improved seed performance. Recent strides in understanding the genetic basis of variation in seed vigor have used genomics and transcriptomics to identify candidate genes for improving germination, and several studies have explored the potential impact of climate change on the percentage and timing of germination. In this review, we discuss these recent advances in the genetic underpinnings of seed performance as well as how climate change is expected to affect vigor in current varieties of staple, vegetable, and other crops.

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“…RNA- Seq technology is a popular sequencing approach in molecular biology, biotechnology, and bioinformatics ( Sun and Wei, 2018 ). This method has been widely exploited in model plants, including Arabidopsis thaliana ( Zhang et al., 2019 ) , Oryza sativa ( Li et al., 2012 ; Pradhan et al., 2019 ; Yang et al., 2021 ), Zea mays ( Xu B et al, 2014 ; Liu et al., 2019 ; Xu et al., 2021 ), Rehmannia glutinosa ( Ma et al., 2021 ), Polygonum cuspidatum ( Wang et al., 2021 ), Asarum sieboldii ( Chen et al., 2021 ), Calotropis gigantea ( Hoopes et al., 2018 ). Transcriptome can be defined as the total number of RNA molecules transcribed from a particular tissue or cell at a given functional or developmental stage, which includes mRNA (messenger RNA) and nc-RNA (non-coding RNA).…”

Section: Introductionmentioning

confidence: 99%

Upcoming progress of transcriptomics studies on plants: An overview

Tyagi

Singh²,

Mathur³

et al. 2022

Front. Plant Sci.

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Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.

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Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq

Cited by 22 publications

References 46 publications

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

Seed germination and vigor: ensuring crop sustainability in a changing climate

Upcoming progress of transcriptomics studies on plants: An overview

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