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Near isogenic lines (NILs) are ideal material for a variety of genetic studies including validation of specific QTL. In the present study, eight pairs of NILs for grain weight were developed, seven in the background of Raj3765, and one in the background of K9107. For this purpose, marker-assisted selection (MAS) was used for the transfer of three grain weight QTL (QGw.ccsu-1A.2, QGw.ccsu-1A.3and QGw.ccsu-1B.1) that were earlier identified in our laboratory. Two genotypes of each of the eight pairs of NILs, differed for QTL alleles (QTLHgwderived from the donor parent and the QTLLgwderived from the recipient parent). Each pair of NILs involved a solitary QTL except one NIL, which differed for all the three QTL. The difference in thousand grain weight (TGW) in two NILs of an individual pair ranged from 2.8 to 7.5 g, thus validating the effect of the QTL for TGW, although the quantum of difference did not always match the phenotypic variance of the corresponding QTL. As expected, the NILs which involved all the three QTL had the maximum difference of 7.5 g in TGW, and the NILs which involved QTL, QGw.ccsu-1A.2had minimum average difference of 2.8 g for TGW. The NILs produced during the present study may be used in future for MAS and for fine mapping of TGW QTL.

Using a suite of morphological traits and neutral molecular markers, we have reevaluated the origins of the two cultivated jute species. The nine Corchorusspecies, which are restricted to both Africa and Asia, were phenotyped for bast fibre yield- and quality-linked traits, morpho-phenetically classified based on those traits’ similarities, genotyped by nuclear microsatellites and haplotyped by chloroplast microsatellites. The two cultivated jute species contain ~70% of the neutral genetic diversity present in their wild relatives. Phylogenetic analyses using 38 highly polymorphic nuclear microsatellites identified C. aestuansas the common ancestor to both the cultivated jute species. C. urticifoliusis the nuclear progenitor of C. olitorius(dark jute), but no close nuclear progenitor of C. capsularis(white jute) could be identified. Although either C. aestuansor C. pseudo-olitoriusor both appear to be the possible cytoplasmic progenitors of white jute, the matrilineal ancestry of dark jute remains obscure. However, the presence of a single, unique chloroplast haplotype in each of the two cultivated species indicates the involvement of other unknown wild relatives. Taken together with archaeobotanical evidence, our results suggest that dark jute had its origin in equatorial region of east Africa, but was domesticated in India. We could not support an Indo-Myanmar origin of white jute, and possibly it also originated in Africa, but was domesticated in Asia.Using a suite of morphological traits and neutral molecular markers, we have reevaluated the origins of the two cultivated jute species. The nine Corchorusspecies, which are restricted to both Africa and Asia, were phenotyped for bast fibre yield- and quality-linked traits, morpho-phenetically classified based on those traits’ similarities, genotyped by nuclear microsatellites and haplotyped by chloroplast microsatellites. The two cultivated jute species contain ~70% of the neutral genetic diversity present in their wild relatives. Phylogenetic analyses using 38 highly polymorphic nuclear microsatellites identified C. aestuansas the common ancestor to both the cultivated jute species. C. urticifoliusis the nuclear progenitor of C. olitorius(dark jute), but no close nuclear progenitor of C. capsularis(white jute) could be identified. Although either C. aestuansor C. pseudo-olitoriusor both appear to be the possible cytoplasmic progenitors of white jute, the matrilineal ancestry of dark jute remains obscure. However, the presence of a single, unique chloroplast haplotype in each of the two cultivated species indicates the involvement of other unknown wild relatives. Taken together with archaeobotanical evidence, our results suggest that dark jute had its origin in equatorial region of east Africa, but was domesticated in India. We could not support an Indo-Myanmar origin of white jute, and possibly it also originated in Africa, but was domesticated in Asia.

Abstract: Amplified fragment length polymorphism (AFLP) analysis was conducted to investigate the level of polymorphism in four jute genotypes including two genotypes (JRC 321 and CMU 010) of Corchorus capsularis (the white jute) and two genotypes (JRO 524 and PPO4) of Corchorus olitorius (the tossa jute). Out of 1024 primer combinations that were tried, as many as 281 combinations of selective primers (13 EcoRI and 64 MseI) were selected, which produced a total of 9092 amplicons, including 752 (8.3%) polymorphic bands in C. capsularis and a total of 8856 amplicons including 1477 (16.7%) polymorphic bands in C. olitorius. The average number of bands/primer combination was 32.3 for C. capsularis and 31.5 for C. olitorius. For C. capsularis, highest polymorphism of 56.6% was shown by primer combination E35M50, while for C. olitorius highest polymorphism of 50% was shown by E41M91. In C. olitorius, 30–50% polymorphism was observed with 27 primer combinations, but in C. capsularis only 3 primer combinations gave this level of polymorphism. Similarly, in C. capsularis <10% polymorphism was detected by 115 primer combinations while in C. olitorius, <10% polymorphism was shown by only 56 primer combinations. These results indicate a higher level of polymorphism in C. olitorius relative to that in C. capsularis. The occurrence of such a large number of polymorphic AFLP markers will facilitate preparation of molecular maps and QTL analysis in jute.

Jute is an important crop of the Indian subcontinent and comprises tossa jute (Corchorus olitorius) and white jute (C. capsularis). The yield and fiber quality of this crop remained stagnant for many years and could not be improved through conventional plant breeding. Also, no effort has been made to develop molecular markers on a scale required for marker‐assisted selection (MAS) to supplement conventional plant breeding. As a first step toward deploying MAS for jute improvement, 2469 simple sequence repeats (SSRs) were developed in tossa jute (JRO 524) using four SSR‐enriched genomic libraries. A random subset of 100 SSRs (25 SSRs from each library) was used to detect polymorphism between the parental genotypes of each of the two recombinant inbred line (RIL) mapping populations. The RILs are being developed from JRO 524 × PPO4 (for fiber fineness) and JRC 321 × CMU 010 (for lignin content) crosses to prepare molecular maps and conduct quantitative trait loci (QTL) analyses. Both SSR length polymorphism and ± polymorphism (null alleles, i.e., presence and absence of specific SSR) were detected; 50 SSRs detected polymorphism between the two genotypes of tossa jute, whereas 45 SSRs detected polymorphism between the two genotypes of white jute. This SSR allelic polymorphism in jute is higher than that reported in other crops and is adequate for construction of genetic maps for QTL analysis. The large‐scale SSRs will also prove useful in studying genetic diversity, population structure, and association mapping.

Six hundred and seventy two loci belonging to 275 expressed sequence tag–simple sequence repeats [EST–SSRs, including 93 wheat (Triticum aestivumL.) and 182 rye (Secale cerealeL.) EST–SSRs] were physically mapped on 21 wheat chromosomes. The mapping involved two approaches, the wet‐lab approach involving use of deletion stocks and the in silico approach involving matching with ESTs that were previously mapped. The number of loci per EST–SSR mapped using the in silico approach was almost double the number of loci mapped using the wet‐lab approach (using deletion stocks). The distribution of loci on the three subgenomes, on the seven homoeologous groups and on the 21 individual chromosomes was nonrandom (P≪ 0.01). Long arms had disproportionately (relative to the difference in DNA content) higher number of loci, with more loci mapped to the distal regions of chromosome arms. A fairly high proportion of EST–SSRs had multiple loci, which were largely (81%) homoeoloci. Rye EST–SSRs showed a high level of transferability (≈77%) to the wheat genome. Putative functions were assigned to 216 SSR‐containing ESTs through homology searches against the protein database. As many as 104 SSR‐containing ESTs (a subset of the above ESTs) were also mapped to the 12 rice chromosomes, which corresponded with the known homology between wheat and rice chromosomes. These physical maps of EST–SSRs should prove useful for comparative genomics, gene tagging, fine mapping, and cloning of genes and QTLs.