Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd (<scp><i>Benincasa hispida</i></scp>)

Hu, Qianmei; Wang, Haiping; Jiang, Biao; Zhu, Huayu; He, Xiaoming; Song, Pengyao; Song, Jiangping; Yang, Sen; Shen, Junjun; Li, Zheng; Hu, Jianbin; Sun, Shouru; Yang, Luming

doi:10.1111/pbr.12990

Cited by 8 publications

(4 citation statements)

References 58 publications

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“…This phenomenon might be attributed to the presence of a mitotic region in close proximity to the centromeric region. The mitotic region contained a significant number of transposable factors and highly repetitive sequences, resulting in a lower density of SSRs near the centromeric region of the chromosome [62,63].…”

Section: Discussionmentioning

confidence: 99%

CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

Li,

Song,

et al. 2023

IJMS

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CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.

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Section: Discussionmentioning

confidence: 99%

CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

Li,

Song,

et al. 2023

IJMS

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“…It has a wide planting range and a long planting history of cultivation. It is one of the most important vegetables transported from southern to northern China (Hu et al 2022). The leaves are responsible for photosynthesis, nutrient distribution, water transport, and gas exchange and are, therefore, considered economically important nutritional organs.…”

Section: Introductionmentioning

confidence: 99%

Fine mapping of BhDDL4.1, a major gene controlling the regulation of the deeply lobed leaf trait in wax gourd (Benincasa hispida)

Bai,

Wang,

Deng

et al. 2024

Preprint

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Lobed leaves play a vital role in high-density cultivation and breeding of wax gourd. Thus, determining the molecular mechanisms underlying the development of lobed leaves is important. To this end, in this study, we aimed to resequence 105 recombinant inbred lines, constructed using the parental lines, GX-7 and my-1, to elucidate the molecular mechanisms underlying leaf development in wax gourd (Benincasa hispida). Genes associated with lobed leaves in wax gourds were first evaluated via quantitative trait loci (QTL) mapping. Next, the F2 population was expanded to 2,000 plants for fine mapping and candidate gene analyses. Thus, the candidate area is reduced to 1.129 Mb, located between the markers InDel980 and InDel853. Functional analyses of candidate genes were performed using gene functional annotation, coding sequence analyses, and expression analyses. Among 48 genes in the candidate region, only Bch04G012650 (termed BhDDL4.1) showed differences in expression between two parents. Using sequence differences of previously screened candidate genes, an InDel marker (InDel623) was developed in BhDDL4.1 for molecular marker-assisted breeding of wax gourd, and the accuracy rate was 74.03%. Our results indicate that BhDDL4.1 may play a key role in regulation of the lobed leaf trait; thereby, we provided a theoretical basis for further exploration of the molecular mechanisms underlying the lobed leaf trait in wax gourds.

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“…(2n = 2x = 24)] is among the most important Cucurbitaceae family crops. These plants are native to China and East India and are the main vegetable varieties in South China and Southeast Asia (Hu et al, 2022). Seed size is an important agronomic characteristic of plants and is important for plant evolution (Angela et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Fine mapping of the major gene BhHLS1 controlling seed size in wax gourd (Benincasa hispida)

Yang,

Wang,

Liu

et al. 2023

Front. Plant Sci.

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Introduction/BackgroundThe seed size of wax gourds is an important agronomic trait; however, the associated genes have not yet been reported.MethodsIn this study, we used a high-density genetic map constructed based on F8 recombinant inbred line populations derived from a cross between MY-1 (large seed) and GX-71 (small seed) strains to detect quantitative trait locis (QTLs) for seed-size-related traits in wax gourd over a two-year period.ResultsTwo stable QTLs (qSL10 and qSW10) for seed length (SL) and seed width (SW) on chromosome 10 were repeatedly detected over two years (2021–2022). qSL10 had a phenotypic variation rate of 75.30% and 80.80% in 2021 and 2022, respectively. Whereas, qSW10 had a phenotypic variation rate of 66.60% and 73.80% in 2021 and 2022, respectively. Further, a single nucleotide polymorphism mutation was found to cause early termination of Bch10G006400 (BhHLS1) translation in GX-71 through sequencing analysis of candidate genes. Based on gene functional annotation and quantitative real-time PCR analyses, BhHLS1 encoded a probable N-acetyltransferase HLS1-like protein and its expression level was significantly different between parents. Therefore, BhHLS1 is a major candidate gene associated with a one-factor polymorphism regulating the SL and SW of wax gourds. Finally, based on variation in the BhHLS1 sequence, a cleaved amplified polymorphic sequence marker was developed for the molecular marker-assisted breeding of wax gourds.DiscussionOverall, this study is of great significance for the genetic improvement of seed size, verification of gene functions, and cultivation of specific germplasm resources for wax gourds.

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Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd (Benincasa hispida)

Cited by 8 publications

References 58 publications

CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

Fine mapping of BhDDL4.1, a major gene controlling the regulation of the deeply lobed leaf trait in wax gourd (Benincasa hispida)

Fine mapping of the major gene BhHLS1 controlling seed size in wax gourd (Benincasa hispida)

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