High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing

Abstract

BackgroundGenetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups.ResultsAn F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance.ConclusionsTo our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.

Evaluation of newly developed SSR markers and identification of quantitative trait loci for bast fibre cellulose in white jute (Corchorus capsularis)

“…Segregation distortion is popularly observed in nearly all intraspecific and inter‐specific genetic linkage maps in plants. In the current study, segregation distortion was found on every linkage group (LG) which corroborated to the segregation result previously reported in jute (Tao et al, ; Topdar et al, ). Also, segregation distortion was found in other crops like sesame (Zhang et al, ).…”

“…585 SSRs (69.14%) showed polymorphism with at least two clear and stable polymorphic fragments in a panel of 24 accessions (Table ). Polymorphic SSRs generated in this study along with other polymorphic markers such as SLAF and InDel markers recently reported by Tao et al () and Zhang et al (), were also used to detect polymorphism between the parent lines and for genotyping of 104 RILs. Of the 5,778 markers, 3,990 (46.42%) primer pairs, [59 (10.1%) SSRs, 10 (8.40%) InDel markers, and 3,921 (77.27%) SLAF markers produced consistent and clear polymorphic bands.…”

“…Electrophoresis and nucleic acid staining were performed according to Zhang et al (). 173 InDel and 5,074 SLAF markers obtained from the previous studies (Tao et al, ; Zhang et al, ) were also tested for polymorphism between the parents of the intraspecific populations. The polymorphic markers were further utilized to determine genotypes among the RILs by PCR amplification as described above.…”

“…However, genetic map and QTL information are very limited to the later one, when compared with that in dark jute. Till date, there have been reported only two cases of linkage maps of which one contains SSR markers (Biswas et al, ; Chen et al, ) and one case of QTL mapping for plant height (Tao et al, ).…”

Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

“…In particular, SLAF-seq e ciently identi es and genotypes large-scale SNPs [20]. SLAF-seq has been applied to many plant species, including spinach [21], sesame [22], walnut [23] soybean [24], cucumber [25], wax gourd [26], cauli ower [27], white jute [28], and maize [29]. SLAF-seq has also been successfully applied to L. vannamei [30].…”