NDLI: A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.)

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A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.)

Content Provider	Springer Nature Link
Author	Kundu, Avijit Chakraborty, Avrajit Mandal, Nur Alam Das, Debajeet Karmakar, Pran Gobinda Singh, Nagendra Kumar Sarkar, Debabrata
Copyright Year	2015
Abstract	We used RAD (restriction-site-associated DNA) sequencing to detect genome-wide SNPs and construct a dense linkage map using an intercross F$_{2}$ population in jute (Corchorus olitorius). The linkage map comprising a total of 503 RAD markers in seven linkage groups spanned 358.5 cM with an average marker interval of 0.72 cM and covered 87.0 % of the genome. Genome-wide segregation distortion of the mapped loci (34.4 %) was non-random across the linkage map, with a directional bias mostly towards the female genotypes. Jute had maximum syntenic relationships with cocoa (47.5 % homology) and diploid cotton (29.2 % homology). However, synteny and collinearity were not conserved. Histological fibre content (FC; total number of fibre cell bundles in a stem cross section) was positively correlated with fibre yield (FY), plant height (PH), root weight (RW) and stem-base diameter (SBD). Broad-sense heritability estimates were high for all traits, with FC and FY showing maximum heritability (~93 %). QTL mapping based on the F$_{2:3}$ phenotypes detected nine QTL across the two environments. The QTL for FC was coincident with one QTL each for FY, PH, RW and SBD on top of a single-SNP (C/T) marker at 40.2 cM on LG1, each accounting for ~7–11 % of the phenotypic variance. Two QTL linked in repulsion one each for PH and SBD, with varying degrees of overdominance, were associated with two single-SNP (C/T) markers on LG2, each accounting for ~17–18 % of the phenotypic variance. Few candidate genes were identified within the QTL regions. Our results would enable development of tools for marker-assisted selection in jute.
Starting Page	1
Ending Page	17
Page Count	17
File Format	PDF
ISSN	13803743
Journal	Molecular Breeding
Volume Number	35
Issue Number	1
e-ISSN	15729788
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-01-20
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Bast fibre Histological fibre content Genomics Jute Linkage map QTL RAD-seq Synteny Plant Sciences Plant Genetics & Genomics Plant Pathology Plant Physiology Biotechnology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Molecular Biology Biotechnology Agronomy and Crop Science

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A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.)