{"doi":"10.3389/fpls.2024.1458294","title":"Integrated analysis of BSA-seq and RNA-seq identified the candidate genes for seed weight in Brassica juncea","abstract":"<jats:sec><jats:title>Introduction</jats:title><jats:p><jats:italic>Brassica juncea</jats:italic> is a major oilseed crop of <jats:italic>Brassica</jats:italic>. The seed weight is one of yield components in oilseed <jats:italic>Brassica</jats:italic> crops. Research on the genetic mechanism of seed weight is not only directly related to the yield and economic value of Brassica juncea but also can provide a theory foundation for studying other Brassica crops.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>To map the genes for seed weight, the parental and F<jats:sub>2</jats:sub> extreme bulks derived were constructed from the cross between the heavy-seeded accession 7981 and the light-seeded one Sichuan yellow (SY) of <jats:italic>B. juncea</jats:italic>, and used in bulk segregant sequencing (BSA-seq). Meanwhile, RNA-sequencing (RNA-seq) was performed for both parents at six seed development stages.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Our results showed that a total of thirty five SNPs were identified in thirty two genes located on chromosomes A02 and A10, while fifty eight InDels in fifty one genes located on A01, A03, A05, A07, A09, A10, B01, B02 and B04. The 7,679 differentially expressed genes were identified in developing seeds between the parents. Furthermore, integrated analysis of BSA-seq and RNA-seq data revealed a cluster of nine genes on chromosome A10 and one gene on chromosome A05 that are putative candidate genes controlling seed weight in <jats:italic>B. juncea</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>This study provides a new reference for research on <jats:italic>Brassica</jats:italic> seed weight and lays a solid foundation for the examination of seed in other <jats:italic>Brassica</jats:italic> crops.</jats:p></jats:sec>","journal":"Frontiers in Plant Science","year":2024,"id":672348,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":492310,"name":"Liu Yang","orcid":"0000-0003-0250-2218","position":1,"is_corresponding":false},{"id":346007,"name":"Lei Kang","orcid":"0000-0001-8729-4547","position":2,"is_corresponding":false},{"id":300086,"name":"Liang You","orcid":null,"position":3,"is_corresponding":false},{"id":242218,"name":"Hao Chen","orcid":"0000-0002-8874-0673","position":4,"is_corresponding":false},{"id":1756678,"name":"Huagui Xiao","orcid":null,"position":5,"is_corresponding":false},{"id":1756679,"name":"Lunwen Qian","orcid":null,"position":6,"is_corresponding":false},{"id":1756680,"name":"Yong Rao","orcid":null,"position":7,"is_corresponding":false},{"id":1756681,"name":"Zhongsong Liu","orcid":null,"position":8,"is_corresponding":false},{"id":1393036,"name":"Bin Yang","orcid":"0000-0003-1947-8058","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Integrated analysis of BSA-seq and RNA-seq identified the candidate genes for seed weight in Brassica juncea","abstract":"<jats:sec><jats:title>Introduction</jats:title><jats:p><jats:italic>Brassica juncea</jats:italic> is a major oilseed crop of <jats:italic>Brassica</jats:italic>. The seed weight is one of yield components in oilseed <jats:italic>Brassica</jats:italic> crops. Research on the genetic mechanism of seed weight is not only directly related to the yield and economic value of Brassica juncea but also can provide a theory foundation for studying other Brassica crops.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>To map the genes for seed weight, the parental and F<jats:sub>2</jats:sub> extreme bulks derived were constructed from the cross between the heavy-seeded accession 7981 and the light-seeded one Sichuan yellow (SY) of <jats:italic>B. juncea</jats:italic>, and used in bulk segregant sequencing (BSA-seq). Meanwhile, RNA-sequencing (RNA-seq) was performed for both parents at six seed development stages.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Our results showed that a total of thirty five SNPs were identified in thirty two genes located on chromosomes A02 and A10, while fifty eight InDels in fifty one genes located on A01, A03, A05, A07, A09, A10, B01, B02 and B04. The 7,679 differentially expressed genes were identified in developing seeds between the parents. Furthermore, integrated analysis of BSA-seq and RNA-seq data revealed a cluster of nine genes on chromosome A10 and one gene on chromosome A05 that are putative candidate genes controlling seed weight in <jats:italic>B. juncea</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>This study provides a new reference for research on <jats:italic>Brassica</jats:italic> seed weight and lays a solid foundation for the examination of seed in other <jats:italic>Brassica</jats:italic> crops.</jats:p></jats:sec>","is_dataset_classified":null,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39698460","pmcid":"PMC11654836","openalex_id":"https://openalex.org/W4405021853","authors":[],"funders":[],"total_grants":0,"fwci":1.15,"citation_percentile":0.77838145,"influential_citations":0,"citation_trend":[{"year":2025,"count":3},{"year":2026,"count":4}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1458294/pdf","host_type":"journal"},{"url":"https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1458294/pdf","host_type":"publisher"},{"url":"https://www.frontiersin.org/articles/10.3389/fpls.2024.1458294/full","host_type":"publisher"},{"url":"https://doi.org/10.3389/fpls.2024.1458294","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39698460","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11654836","host_type":"repository"},{"url":"https://doaj.org/article/c785b966c6ab4677987858b2f760a1fc","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11654836/pdf/fpls-15-1458294.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11654836","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11654836?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Photosynthetic Processes and Mechanisms","Plant Disease Resistance and Genetics","Plant nutrient uptake and metabolism"],"mesh_terms":[],"keywords":["Brassica","RNA-Seq","Biology","Gene","Genetics","Computational biology","Candidate gene","Transcriptome","Biotechnology","Botany","Gene expression","Brassica juncea","seed weight","Candidate Genes","Bsa-seq"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pfam"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-16T08:44:19.604819Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}