Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Jiang, Xueqian; Yang, Xijiang; Zhang, Fan; Yang, Tianhui; Yang, Ching Hong; He, Fei; Gao, Ting; Wang, Chuan; Yang, Qingchuan; Wang, Zhen

doi:10.1186/s12870-022-03864-7

Cited by 13 publications

(12 citation statements)

References 71 publications

(82 reference statements)

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“…Since drought tolerance involves complicated metabolic and signaling pathways, future studies should analyze transcriptome rather than single gene families to better reveal the molecular mechanism of drought tolerance. Additionally, transcriptome analysis has been combined with QTL mapping to facilitate candidate gene discovery such as for leaf development in alfalfa ( Jiang et al., 2022 ), hypocotyl elongation in rapeseed ( Luo et al., 2017 ), pericarp thickness in sweet corn ( Wu et al., 2020 ), and heat-tolerance in tomato ( Wen et al., 2019 ) to facilitate candidate gene discovery. Joint QTL mapping and transcriptome analysis can be potentially useful for dissecting the genetic architecture of drought tolerance in blueberries.…”

Section: Discussion: Limitations Of Previous Studies and Directions F...mentioning

confidence: 99%

Review on blueberry drought tolerance from the perspective of cultivar improvement

Ru,

Sanz-Saez,

Leisner

et al. 2024

Front. Plant Sci.

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Blueberry (Vaccinium spp.) is an increasingly popular fruit around the world for their attractive taste, appearance, and most importantly their many health benefits. Global blueberry production was valued at $2.31 billion with the United States alone producing $1.02 billion of cultivated blueberries in 2021. The sustainability of blueberry production is increasingly threatened by more frequent and extreme drought events caused by climate change. Blueberry is especially prone to adverse effects from drought events due to their superficial root system and lack of root hairs, which limit blueberry’s ability to intake water and nutrients from the soil especially under drought stress conditions. The goal of this paper is to review previous studies on blueberry drought tolerance focusing on physiological, biochemical, and molecular drought tolerance mechanisms, as well as genetic variability present in cultivated blueberries. We also discuss limitations of previous studies and potential directions for future efforts to develop drought-tolerant blueberry cultivars. Our review showed that the following areas are lacking in blueberry drought tolerance research: studies of root and fruit traits related to drought tolerance, large-scale cultivar screening, efforts to understand the genetic architecture of drought tolerance, tools for molecular-assisted drought tolerance improvement, and high-throughput phenotyping capability for efficient cultivar screening. Future research should be devoted to following areas: (1) drought tolerance evaluation to include a broader range of traits, such as root architecture and fruit-related performance under drought stress, to establish stronger association between physiological and molecular signals with drought tolerance mechanisms; (2) large-scale drought tolerance screening across diverse blueberry germplasm to uncover various drought tolerance mechanisms and valuable genetic resources; (3) high-throughput phenotyping tools for drought-related traits to enhance the efficiency and affordability of drought phenotyping; (4) identification of genetic architecture of drought tolerance using various mapping technologies and transcriptome analysis; (5) tools for molecular-assisted breeding for drought tolerance, such as marker-assisted selection and genomic selection, and (6) investigation of the interactions between drought and other stresses such as heat to develop stress resilient genotypes.

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Section: Discussion: Limitations Of Previous Studies and Directions F...mentioning

confidence: 99%

Review on blueberry drought tolerance from the perspective of cultivar improvement

Ru,

Sanz-Saez,

Leisner

et al. 2024

Front. Plant Sci.

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“…Jiang et al [ 121 ] mapped leaf length, leaf width, and leaf area, traits that influence alfalfa forage yield and quality, in an F 1 mapping population derived from a cross of a cultivar named ‘Zhongmu No.1’ that is characterized by large leaf area and a landrace named ‘Cangzhou’ which expresses a smaller leaf area. Using a combination of QTL mapping, RNA-seq analysis, and qRT-PCR, they identified seven candidate genes associated with leaf development in five major QTL regions [ 121 ]. Their study underlines the importance of landraces and provides a basis for marker-assisted breeding.…”

Section: Application Of New Genomic Technologies In Landraces and Ind...mentioning

confidence: 99%

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Lazaridi,

Kapazoglou,

Gerakari

et al. 2024

Plants

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Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

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“…Therefore, by combining QTL mapping with RNA-seq data, candidate genes can be screened e ciently and accurately using pathway analysis of differentially expressed genes. (Jiang et al 2022a;Song et al 2021). Presently, it is extensively utilized for screening potential genes associated with traits in plants such as brassica napus (Song et (Huang et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

Chai,

Yang,

Shi

et al. 2023

Preprint

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Hull color is a crucial characteristic that helps assess the nutritional value and economic potential of foxtail millet. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for hull color are limited. Here, we mapped QTLs responsible for hull color by using 215 recombinant inbred lines (RILs) derived from Yugu 18 (Light yellow hull) × Hongjiugu (Red hull) and a high-density bin map. A total of 36 QTLs for hull color were detected in all four environments by four phenotypic evaluation methods. Among these QTLs, a major QTL for hull color (HC) named qHC1.2 was repeatedly mapped on chromosome 1 and explained 8.89 – 69.63% of the phenotypic variation. In addition, RNA sequencing (RNA-seq) was performed 7, 14, and 21 days after flowering for the YRRIL-145 and YRRIL-229, and three differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Among them, DEGs, only one gene, Seita.1G057300, encoding a cinnamyl alcohol dehydrogenase (CAD), was located in the candidate region of qHC1.2. Furthermore, sequence analysis revealed One SNP (A to G), located at the third exon, resulted in an amino acid change from isoleucine to valine in YRRIL-145 compared with YRRIL-229. Our results provide a foundation for further cloning of qHC1.2 and will be very useful in clarifying the regulatory mechanism for hull color synthesis in foxtail millet.

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Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Cited by 13 publications

References 71 publications

Review on blueberry drought tolerance from the perspective of cultivar improvement

Review on blueberry drought tolerance from the perspective of cultivar improvement

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

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