Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon

Zhang, Hong; Zhang, Xuejun; Li, Meihua; Yang, Yong; Li, Zhiqiang; Xu, Yuhui; Wang, Haojie; DengMing, Wang; Zhang, Yongbing; Wang, Huaisong; Fu, Qihua; Zheng, Jing; Huiuk, Yi

doi:10.1016/j.ygeno.2022.110306

Cited by 8 publications

(11 citation statements)

References 82 publications

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“…The high-density genetic maps based on re-sequencing constructed by bin markers have shown that continuous SNPs without recombination in one bin marker have been realized in many crops ( Li et al., 2016 ; Lu et al., 2017 ; Han K, et al, 2018 ; Tong et al., 2020 ), including leguminous species ( Agarwal et al., 2018 ; Agarwal et al., 2019 ; Garg et al., 2022 ). In General, a population containing 100–400 individuals harbors 1000–4000 bins ( Zhang H, et al, 2022 ), indicating that the QTL mapping resolution for a species with a genome size above 2 Gb may approximate hundreds of kilobases ( Zhang et al., 2022 ). We obtained 2494 bins in total with 1008 kb per bin on average ( Figure 4A ; Table S4 ), where four out of five QTL regions were under 5 Mb ( Table 1 ), indicating that a high mapping resolution had been achieved.…”

Section: Discussionmentioning

confidence: 99%

“…As thermophilic crops, peanuts require relatively high temperatures throughout their development ( Wang et al., 2003 ). Cold injury causes different degrees of damage to peanuts during germination, seedling emergence, flowering, maturity, and other key growth stages ( Zhang X, et al, 2022 ). Among these, damage at the germination stage is known to be a common occurrence.…”

Section: Introductionmentioning

confidence: 99%

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Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

Zhang

Wang

et al. 2023

Front. Plant Sci.

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Low temperatures significantly affect the growth and yield of peanuts. Temperatures lower than 12 °C are generally detrimental for the germination of peanuts. To date, there has been no report on precise information on the quantitative trait loci (QTL) for cold tolerance during the germination in peanuts. In this study, we developed a recombinant inbred line (RIL) population comprising 807 RILs by tolerant and sensitive parents. Phenotypic frequencies of germination rate low-temperature conditions among RIL population showed normally distributed in five environments. Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. The cold tolerance-related QTLs were repeatedly detected in all five environments, and the genetic distance was 6.01 cM (46.74 cM - 61.75 cM) after taking a union set. To further confirm that qRGRB09 was located on chromosome B09, we developed Kompetitive Allele Specific PCR (KASP) markers for the corresponding QTL regions. A regional QTL mapping analysis, which was conducted after taking the intersection of QTL intervals of all environments into account, confirmed that qRGRB09 was between the KASP markers, G22096 and G220967 (chrB09:155637831–155854093), and this region was 216.26 kb in size, wherein a total of 15 annotated genes were detected. This study illustrates the relevance of WGRS-based genetic maps for QTL mapping and KASP genotyping that facilitated QTL fine mapping of peanuts. The results of our study also provided useful information on the genetic architecture underlying cold tolerance during germination in peanuts, which in turn may be useful for those engaged in molecular studies as well as crop improvement in the cold-stressed environment.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

Zhang

Wang

et al. 2023

Front. Plant Sci.

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“…The location of genes controlling seed germination traits has been extensively studied in other crops, with significant discoveries made in rice (Liu et al, 2016 ), wheat (Zheljazkov et al, 2021 ), and maize (Zhang et al, 2022a ). In terms of Cucumis melo L., a QTL analysis for the seed size trait has already been conducted (Zhang et al, 2022b ). Using genome-wide association analysis in Solanum lycopersicum , the SIMAPK11 was identified to regulate seed dormancy, indicating that the ABA pathway was involved in seed dormancy and germination.…”

Section: Discussionmentioning

confidence: 99%

“…Extensive research has been conducted on the effects of different exogenous treatments on melon seed germination. Salt, alkali, germination initiation treatments, and hormone treatments significantly affect melon seed germination and seedling production (Barrero et al, 2009 ; Castañares and Bouzo, 2019 ; Saberali and Shirmohamadi-Aliakbarkhani, 2020 ; Zhang et al, 2022b ).…”

Section: Introductionmentioning

confidence: 99%

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A preliminary mapping of QTL qsg5.1 controlling seed germination in melon (Cucumis melo L.)

Yang

Dai

et al. 2022

Front. Plant Sci.

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Melon (Cucumis melo L.) seed germination significantly affects its economic value. Cultivation of melon varieties with high germination ability and seedling vigor is beneficial in large-scale melon propagation. In this study, two melon genotypes differing in their germination ability, P5 with low and P10 with high germination ability, were used to identify the optimal seed germination conditions by evaluating different water immersion times and germination temperatures. The germination rate of the P5 and P10 parental genotypes and their segregating population, consisting of 358 F2:3 families, were evaluated for 2 years to identify their genetic basis. QTL analysis was performed on a high-density genetic map constructed using specific-locus amplified fragment sequencing (SLAF-seq). The germination rate of F1 and F2 populations treated with water immersion for 8 h at 28°C and measured at 48 h showed a normal distribution Genetic mapping carried out using the high-density genetic map revealed eight QTLs in chromosomes 2, 4, 5, 6, and 8 that control melon seed germination, of which 2020/2021-qsg5.1 was consistently significant in both years of experimentation. qsg5.1 explained 15.13% of the phenotypic variance with a LOD of 4.1. To fine map the candidate region of qsg5.1, eight cleaved amplified polymorphism sequence (CAPS) markers were used to construct a genetic map with another 421 F2 individual fruits. The major QTL qsg5.1 was located between SNP53 and SNP54 within a 55.96 Kb interval containing four genes. qRT-PCR gene expression analysis of the candidate genes showed that MELO3C031219.2 (Phosphorus transporter PHO-5) exhibited a significant difference in gene expression between the parental lines at 24, 32, and 48 h after germination, potentially being the underlying gene controlling melon seed germination. These results provide a theoretical basis for the molecular mechanisms controlling melon seed germination and can practically contribute to further improving germination to increase the propagation efficiency of commercial melon cultivars.

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Melon (Cucumis melo L.): Genomics and Breeding

Chikh-Rouhou¹,

Abdedayem²,

Solmaz³

et al. 2023

Smart Plant Breeding for Vegetable Crops in Post-Genomics Era

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Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon

Cited by 8 publications

References 82 publications

Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

A preliminary mapping of QTL qsg5.1 controlling seed germination in melon (Cucumis melo L.)

Melon (Cucumis melo L.): Genomics and Breeding

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