Conjunctive Analyses of BSA-Seq and BSR-Seq Unveil the Msβ-GAL and MsJMT as Key Candidate Genes for Cytoplasmic Male Sterility in Alfalfa (Medicago sativa L.)

Abstract

Knowing the molecular mechanism of male sterility in alfalfa is important to utilize the heterosis more effectively. However, the molecular mechanisms of male sterility in alfalfa are still unclear. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-seq (BSR) were performed with F2 separation progeny to study the molecular mechanism of male sterility in alfalfa. The BSA-seq analysis was located in a candidate region on chromosome 5 containing 626 candidate genes which were associated with male sterility in alfalfa, while the BSR-seq analysis filtered seven candidate DEGs related to male sterility, and these candidate genes including EF-Tu, β-GAL, CESA, PHGDH, and JMT. The conjunctive analyses of BSR and BSA methods revealed that the genes of Msβ-GAL and MsJMT are the common detected candidate genes involved in male sterility in alfalfa. Our research provides a theory basis for further study of the molecular mechanism of male sterility in alfalfa and significant information for the genetic breeding of Medicago sativa.

Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut

“…BSA-seq has been widely used to map the QTL of target traits in crop species [18,36] Some studies have reported that BSA-seq can be combined with other techniques to fur ther reveal key functional candidate genes, such as with RNA-Seq, BSR-seq, and the link age mapping approach [17,18,20]. In this study, the combination of BSA-seq and SSR markers was used for the first time to identify QTL conferring resistance to RFS.…”

“…At present, with the development of sequencing technologies and the availability of reference genome sequences of rice, bulked segregant analysis with whole genome resequencing (BSA-seq) is considered an efficient and cost-effective method to rapidly locate genomic regions containing genes or QTLs affecting target traits [17,18]. This method has been successfully used in several plant species, including Oryza sativa [18,19], Medicago sativa L. [18], Cucurbita pepo [20], and Zea mays [21].…”

“…At present, with the development of sequencing technologies and the availability of reference genome sequences of rice, bulked segregant analysis with whole genome resequencing (BSA-seq) is considered an efficient and cost-effective method to rapidly locate genomic regions containing genes or QTLs affecting target traits [17,18]. This method has been successfully used in several plant species, including Oryza sativa [18,19], Medicago sativa L. [18], Cucurbita pepo [20], and Zea mays [21]. Compared to traditional linkage mapping, in which offspring are individually genotyped and phenotyped, BSA requires fewer samples for genotyping because only individuals representing the extreme phenotypes of the population need to be identified [22].…”

Conjunctive Analyses of BSA-Seq and BSR-Seq to Identify Candidate Genes Controlling the Black Lemma and Pericarp Trait in Barley

“…However, BSR analysis generally requires a high-quality reference genome, which reduces its efficiency in species with complex genomes. Thus, the combination of BSA and BSR takes advantage of both methods to improve the accuracy and efficiency of mapping [30][31][32].…”