A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.)

Topdar, Niladri; Kundu, Avijit; Sinha, Manish Kumar; Sarkar, Debabrata; Das, Moumita; Banerjee, Sourav; Kar, C. S.; Satya, Pratik; Balyan, H. S.; Mahapatra, B. S.; Gupta, P. K.

doi:10.3103/s0095452713030092

Cited by 33 publications

(19 citation statements)

References 43 publications

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“…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, ).…”

Section: Discussionsupporting

confidence: 93%

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

Niyitanga

Ibrahim

et al. 2019

Plant Breeding

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Cellulose is one of the main chemical component of bast fibre in jute. However, quantitative trait loci (QTL) for bast fibre cellulose content remains elusive. In this study, we identified 846 new SSR markers from 70,792 unigenes in the NCBI and validated them in a panel of 24 diverse jute accessions. Of 846 SSRs, 748 (88.41%) were successfully amplified, and 585 (69.14%) showed polymorphisms, implying that these are high‐quality SSRs. Furthermore, 585 SSRs along with 5,074 polymorphic SLAF (specific locus amplified fragment) and 173 InDel markers were used to reconstruct a high‐dense linkage map in a recombinant inbred population with 104 F8 lines. Totally, 835 markers were successfully mapped to a whole length of 604.5 cM with a mean distance of 2.84 cM between adjacent markers. Furthermore, five QTLs for bast fibre cellulose were identified. One major QTL (qBFC1‐1) was stable in 2 years and explained average phenotypic variance with 14.34%. These results may be useful for developing enhanced bast fibre quality in white jute through marker‐assisted selection (MAS) breeding.

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Section: Discussionsupporting

confidence: 93%

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

Niyitanga

Ibrahim

et al. 2019

Plant Breeding

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“…The rate was higher than those reported by Das et al [20] and Topdar et al [16]. Segregation distortion is widespread in inter-specific and intra-specific crosses used to construct mapping populations [45].…”

Section: Discussionmentioning

confidence: 92%

“…Although genetic maps for jute exist, the total number of markers on the LGs is limited [16–19], and do not provide comprehensive coverage of the jute genome. In general, a high number of polymorphic markers is necessary to guarantee the accuracy of a linkage map [2].…”

Section: Discussionmentioning

confidence: 99%

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

Tao

Huang

et al. 2017

BMC Genomics

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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.

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“…Several jute linkage maps have been previously developed with successive adoption of new molecular marker technologies (Das et al 2012;Topdar et al 2013). The linkage map constructed in the present study exhibits a regular marker distribution, but a significantly longer cumulative genetic map (2016 cM).…”

Section: Genetic Linkage Mappingmentioning

confidence: 99%

Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis)

et al. 2015

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Jute is the most important bast fibre crop of the world. Stem rot disease caused by Macrophomina phaseolina is a major constraint of jute cultivation. Recent advances in genomics and bioinformatics have enabled the development of highthroughput genotyping, allowing the construction of saturated linkage maps for identification of resistant lines. In the present study, single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs) were developed and were used to generate comprehensive linkage maps for Corchorus capsularis. From a set of 43,335 variant nucleotide positions detected through in silico analysis, 768 SNPs were selected for genotyping of a recombinant inbred line population. A total of 705 SNPs (91.7 %) successfully detected segregating polymorphisms. In addition to EST-SNPs, genomic simple sequence repeats were assigned to the genetic map in order to obtain an evenly distributed genome-wide coverage. Nine linkage groups were constructed from genetic maps with estimated cumulative total map length of 2016 cM and average inter-locus interval of 4.2 cM. SNP assay and linkage mapping are important set of tools for marker-assisted selection, and it could be used for identifying resistance to M. phaseolina in jute cultivars. This is the first report of developing SNP markers and SNP-based linkage map in jute.

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A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.)

Cited by 33 publications

References 43 publications

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

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

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

Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis)

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