Physical mapping of wheat and rye expressed sequence tag-simple sequence repeats on wheat chromosomes

Six hundred and seventy two loci belonging to 275 expressed sequence tag-simple sequence repeats [EST-SSRs, including 93 wheat (Triticum aestivum L.) and 182 rye (Secale cereale L.) 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. Dna-based molecular markers, particularly SSRs, have been developed and mapped on chromosomes in a variety of crop plants. In bread wheat, genetic and physical mapping of SSRs has been an ongoing exercise, and, to date, ≈2450 SSRs (1 SSR 1.63 cM-1) have been genetically mapped (for details see Torada et al., 2006) and ≈1320 SSRs (62 SSRs chromosome-1) have been physically mapped (for details see Goyal et al., 2005). With a genome size of ≈16 000 Mbp, it is evident that despite concerted efforts, the density of mapped SSRs in bread wheat remains relatively low and continued efforts are needed to increase the density of these SSRs on available genetic and physical maps. In recent years, emphasis has also shifted from genomic SSRs to EST-SSRs due to the availability of very large databases of ESTs from all of the cereals including bread wheat. Consequently, the number of EST-SSRs in cereals now includes 43 598 from bread wheat (Peng and Lapitan, 2005), 16 917 from rice and 184 from rye (La Rota et al., 2005; Hackauf and Wehling, 2002). The genetic mapping of these EST-SSRs is difficult due to a low level of polymorphism, as a result of their conserved nature. Physical mapping of these EST-SSRs in wheat is equally difficult due to the occurrence of homoeoloci exhibiting no polymorphism. This has discouraged wheat researchers from undertaking a large-scale project to genetically or physically map wheat EST-SSRs although genetic mapping of 325 EST-SSRs (Gao et al., 2004; Nicot et al., 2004; Yu et al., 2004) and physical mapping of 305 EST-SSRs was recently undertaken (Yu et al., 2004; Zhang et al., 2005; Peng and Lapitan, 2005). We previously reported genetic mapping of 58 and physical mapping of 270 genomic SSRs (Gupta et al., 2002; Goyal et al., 2005). The present study is an extension of our earlier studies on physical mapping of SSRs and involved both wet-lab and in silico approaches, leading to the successful mapping of as many as 672 loci. The in silico approach allowed mapping of twice the number of loci (per EST-SSR) mapped using wet-lab analysis

Development and characterization of large-scale simple sequence repeats 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

Development of SSR markers and construction of a linkage map in jute

Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources. We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute

DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum

Background: The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps. Results: A high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells. Conclusions: The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.Keywords: Physical mapping, Deletion mutant, Non homologous end joining, Wheat chromosome 3B, Chromatin\, , Radiation hybrid, Gamma radiatio

QTL Analysis for Drought Tolerance in Wheat: Present Status and Future Possibilities

In recent years, with climate change, drought stress has been witnessed in many parts of the world. In many irrigated regions also, shortage of water supply allows only limited irrigation. These conditions have an adverse effect on the productivity of many crops including cereals such as wheat. Therefore, genetics of drought/water stress tolerance in different crops has become a priority area of research. This research mainly involves use of quantitative trait locus (QTL) analysis (involving both interval mapping and association mapping) for traits that are related to water-use efficiency. In this article, we briefly review the available literature on QTL analyses in wheat for traits, which respond to drought/water stress. The outlook for future research in this area and the possible approaches for utilizing the available information on genetics of drought tolerance for wheat breeding are also discussed

Orthology between genomes of Brachypodium, wheat and rice

BACKGROUND: In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. FINDINGS: Comparative sequence analysis of 3,818 Brachypodium EST (bEST) contigs and 3,792 physically mapped wheat EST (wEST) contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. CONCLUSION: The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals

Mapping main effect QTL and epistatic interactions for leaf rust and yellow rust using high density ITMI linkage map

The present study was undertaken to identify QTL for leaf rust (LR) and stripe or yellow rust (YR) using ITMI-mapping population under Indian environmental conditions. A high density framework linkage map consisting of 1,345 markers was used to conduct single and two locus QTL analyses using QTLCartographer and QTLNetwork. A total of 14 main-effect QTL (M-QTL) for LR and 12 M-QTL for YR were detected. Among all these M-QTL, 7 for LR and 4 for YR were novel, and have not been reported in earlier studies using same population. Eight significant Q×Q interactions for each trait were also identified, which involved 16 epistatic-QTL (E-QTL) for LR and 14 E-QTL (including 2 M-QTL) for YR. Four genomic regions had QTL for both LR and YR. The phenotypic variation explained (PVE) ranged from 2.16% - 29.07% for M-QTLLR and from 0.80%-7.05% for E-QTL. Epistasis contributed a significant portion of the PVE (26.01% for LR and 31.51% YR) for the two traits. Minor environment interactions were observed for YR

An integrated physical map of simple sequence repeats in bread wheat

Physical mapping of DNA-based markers in wheat has been greatly facilitated due to the availability of deletion stocks, which constitute an ideal material for mapping these markers to specific chromosomal regions or bins to create physical landmarks. In the present study, the available physical maps for wheat SSRs were enriched by addition of 128 new SSR loci that belonged to wheat gSSRs and brachypodium gSSRs and EST-SSRs. This led to the development of an integrated physical map of 2,031 wheat SSR loci. A maximum of 765 loci (37.67%) were mapped on sub-genome B followed by the 651 loci (32.05%) on sub-genome D and 615 loci (30.28%) on sub-genome A, thus giving a mean resolution of 7.8 Mb between any two SSR loci. Relative to genomic SSRs (gSSRs), the EST-SSRs of brachypodium showed greater transferability in cv. Chinese Spring. Using 704 SSR loci which were mapped genetically as well as physically, a comparison was made between genetic and physical maps to determine the distribution of recombination frequencies (cM/Mb) in different regions of the wheat genome. Recombination frequencies within the individual bins ranged from 0.01 cM/Mb (low recombination) to 13.16 cM/Mb (high recombination), suggesting an uneven distribution along the chromosomes or chromosome arms. Hopefully, the integrated physical map presented in this communication may prove useful in the currently on-going whole genome sequencing of wheat genome through alignment of BAC contigs. A comparison of integrated physical map with genetic linkage map will also facilitate on-going and future genomics research

High density digital recording

In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat