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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.)

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Abstract

We used RAD (restriction-site-associated DNA) sequencing to detect genome-wide SNPs and construct a dense linkage map using an intercross F2 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 F2:3 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.

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Abbreviations

bfs:

Bast fibre-shy

FC:

Fibre content

FCB:

Fibre cell bundle

FY:

Fibre yield

LG:

Linkage group

PH:

Plant height

QTL:

Quantitative trait loci

RAD-seq:

Restriction-site-associated DNA sequencing

RW:

Root weight

SBD:

Stem-base diameter

SG:

Sudan Green

SNP:

Single nucleotide polymorphism

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Acknowledgments

We acknowledge the Xcelris Labs Ltd., Ahmedabad, for assistance in Illumina HiSeq 2000 sequencing, raw data processing and the related bioinformatics analyses. We thank Director, Sugarcane Breeding Institute (SBI), Coimbatore, for allowing us to advance the mapping population in the off-season nursery, Dr. N. Subramonian (SBI, Coimbatore) for extending laboratory facilities for DNA isolation and Surajeet Dey (CRIJAF, Barrackpore) for field assistance in the development and maintenance of the mapping populations. The research was funded by National Fund for Basic, Strategic and Frontier Application Research in Agriculture (NFBSFARA), Indian Council of Agricultural Research (ICAR), New Delhi (F. No. NFBSFARA/GB-2018/2011-12), and ICAR Network Project of Transgenics in Crops (ICAR-NPTC), ICAR, New Delhi (F. No. ICAR/NRCPB/NPTC-3052). Comments and suggestions on the manuscript from two anonymous reviewers are gratefully acknowledged.

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  1. Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata, 700 120, West Bengal, India

    Avijit Kundu, Avrajit Chakraborty, Nur Alam Mandal, Debajeet Das, Pran Gobinda Karmakar & Debabrata Sarkar

  2. ICAR-National Research Centre on Plant Biotechnology (NRCPB), Pusa, New Delhi, 110 012, India

    Nagendra Kumar Singh

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  1. Avijit Kundu
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Kundu, A., Chakraborty, A., Mandal, N.A. et al. 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.). Mol Breeding 35, 19 (2015). https://doi.org/10.1007/s11032-015-0249-x

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