Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed

Li, Xiaodong; Liu, Xumei; Fan, Yonghai; Li, Shengting; Yu, Mengna; Qian, Mingchao; Chen, Yuling; Chen, Hongqiao; Li, Xinchun; Liu, Bei; Xu, Xinhua; Qu, Cunmin; Li, Jiana; Lu, Kun

doi:10.1016/j.cj.2022.08.008

Cited by 5 publications

(5 citation statements)

References 80 publications

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“…Phenotypic and statistical analyses were performed to explore the genetic foundations of the main inflorescence flower bud cluster traits. The main inflorescence flower bud clustering trait of Brassica napus was clarified genetically using the (BSA) whole-genome resequencing approach and preliminary location of the major genes that influence it [14]. On this basis, candidate genes were predicted using bioinformatics analysis to locate the region.…”

Section: Introductionmentioning

confidence: 99%

Mapping and candidate gene analysis of clustered bud on the main inflorescence in Brassica napus L.

et al. 2023

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Breeding rapeseed varieties with more main inflorescence siliques is an idea for developing rapeseed varieties that are suitable for light and simplified cultivation. The Brassica napus exhibited cluster bud of the main inflorescence (Bnclib) gene. At the fruiting stage, the main inflorescence had more siliques, higher density, and more main inflorescences. Moreover, the top of the main inflorescence bifurcated. Genetic analysis showed that the separation ratio between Bnclib and the wild type in the F2 generation was 3:1, which indicated that the trait was a single-gene-dominant inheritance. Among the 24 candidate genes, only one gene, BnaA03g53930D, showed differential expression between the groups (False discovery rate, FDR ≤ 0.05, |log2FC|≤ 1). qPCR verification of the BnaA03g53930D gene between Huyou 17 and its Bnclib near-isogenic line showed that BnaA03g53930D was significantly differentially expressed in the stem tissue of Huyou 17 and its Bnclib near-isogenic line (Bnclib NIL). The determination of gibberellin (GA), brassinolide (BR), cytokinin (CTK), jasmonic acid (JA), growth hormone (IAA), and strigolactone (SL) content in the shoot apex of Huyou 17 by Bnclib NIL and wild type showed that all six hormones significantly differed between the Bnclib NIL and Huyou 17. It is necessary to conduct further research on the interactions between JA and the other five hormones and the main inflorescence bud clustering in B. napus.

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Section: Introductionmentioning

confidence: 99%

Mapping and candidate gene analysis of clustered bud on the main inflorescence in Brassica napus L.

et al. 2023

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“…Three of the variants occurred in the non-coding region, including one in the 5 ′ -UTR and two in the 3 ′ -UTR; and other five variants were identified in the coding region, including three synonymous and two missense mutations. SNPs in the coding region may alter the amino acid, affecting the structure and function of the corresponding proteins [22], ultimately leading to changes in the wool phenotype. In this study, we found that SNP3 and SNP5 in the coding region were missense mutations, the conversion of GTG codon to GCG codon in SNP3 resulted in the change of valine to alanine, thus p.Val17Ala, and the conversion of GAC codon to AAC codon in SNP5 resulted in the change of aspartic acid to asparagine, that is, p.Asp317Asn, and both SNPs were significantly associated with CVFD and MFC were significantly correlated, which may be due to the change in amino acid leading to the change in protein secondary structure, which in turn leads to the change in phenotype.…”

Section: Discussionmentioning

confidence: 99%

Expression Localization of the KRT32 Gene and Its Association of Genetic Variation with Wool Traits

Chen,

Zhao,

et al. 2024

CIMB

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Changes in keratin gene expression and spatiotemporal regulation determine the compositional content and cellular localization of wool keratin, thereby affecting wool traits. Therefore, keratin gene family member 32 (KRT32) was selected for a study using RT-qPCR, immunofluorescence, and penta-primer amplification refractory mutation system (PARMS) techniques. The results showed that KRT32 mRNA was highly expressed in the skin and localized to the inner root sheath (IRS), outer root sheath (ORS) and dermal papilla (DP). Sequencing results identified eight SNPs in KRT32, and association analyses revealed that the variations were significantly associated with multiple traits in wool (p < 0.05), including MFD, CF and MFC. The constructed haplotype combination H2H3 has higher CF and smaller MFD than other haplotype combination (p < 0.05). In conclusion, KRT32 can be used as a candidate gene for molecular genetic improvement of wool in Gansu Alpine Fine-wool sheep.

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“…17 Leveraging high-throughput sequencing, from the development of crop genome maps to the identification of high-quality gene resources and the application of molecular marker-assisted breeding, crop breeding efficiency can be enhanced by thousands of times, while breeding cycles can be shortened to two-thirds of their original duration, ultimately enabling the rapid selection of high-quality, environmentally friendly, and nutrient-use-efficient new varieties. 18 2.3.2. Ensuring the Quality of Agricultural Products.…”

Section: Primary Application Scenarios and Objectives Of Bioagricultu...mentioning

confidence: 99%

“…Taking maize as an example, agricultural enterprises have the highest efficiency, followed by farmers’ professional cooperatives and family farms, with professional large-scale households recording the lowest average production efficiency . Leveraging high-throughput sequencing, from the development of crop genome maps to the identification of high-quality gene resources and the application of molecular marker-assisted breeding, crop breeding efficiency can be enhanced by thousands of times, while breeding cycles can be shortened to two-thirds of their original duration, ultimately enabling the rapid selection of high-quality, environmentally friendly, and nutrient-use-efficient new varieties …”

Section: Necessity For the Development Of Bioagriculture In Chinamentioning

confidence: 99%

Pathways to Ensuring Food Security in the Context of the Chinese Bioeconomy Landscape

Chen,

Pu,

Luo

et al. 2024

ACS Agric. Sci. Technol.

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Recently, China released its first 5-year plan for bioeconomy development, in which bioagriculture was identified as one of the five key development areas. It not only aims to cultivate new momentum for ensuring food security in China but also outlines a new direction for agro-biotechnology innovation and the development of the bioindustry. This paper elaborates on the significance of agriculture as a crucial application scenario in the future bioeconomy and analyzes the demand for agricultural biotechnology in the context of China's food security. Additionally, it summarizes the development experiences of countries and regions, such as the United States and the European Union in the field of bioeconomy, including their strategic policies, leading technologies, and policy impacts. The paper further proposes specific ways to fully leverage the supportive role of bioeconomy in ensuring China's food security. These methods encompass the enhancement of agricultural biotechnology innovation capabilities, the application of biotechnological achievements in agriculture, and the refinement of the regulatory framework for biotechnology.

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Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed

Cited by 5 publications

References 80 publications

Mapping and candidate gene analysis of clustered bud on the main inflorescence in Brassica napus L.

Mapping and candidate gene analysis of clustered bud on the main inflorescence in Brassica napus L.

Expression Localization of the KRT32 Gene and Its Association of Genetic Variation with Wool Traits

Pathways to Ensuring Food Security in the Context of the Chinese Bioeconomy Landscape

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