A draft physical map of a D-genome cotton species (Gossypium raimondii)

<p>Abstract</p> <p>Background</p> <p>Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, <it>Gossypium hirsutum </it>and <it>G. barbadense</it>, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor <it>Gossypium raimondii </it>for complete sequencing.</p> <p>Results</p> <p>A whole genome physical map of <it>G. raimondii</it>, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to <it>Arabidopsis thaliana </it>(AT) and <it>Vitis vinifera </it>(VV) whole genome sequences.</p> <p>Conclusion</p> <p>Several lines of evidence suggest that the <it>G. raimondii </it>genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the <it>Arabidopsis </it>and <it>Vitis vinifera </it>genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.</p

Identification and Expression Profiling of the <i>Regulator of Chromosome Condensation 1 (RCC1)</i> Gene Family in <i>Gossypium Hirsutum</i> L. under Abiotic Stress and Hormone Treatments

The regulator of chromosome condensation 1 (RCC1) is the nucleotide exchange factor for a GTPase called the Ras-related nuclear protein, and it is important for nucleo-plasmic transport, mitosis, nuclear membrane assembly, and control of chromatin agglutination during the S phase of mitosis in animals. In plants, RCC1 molecules act mainly as regulating factors for a series of downstream genes during biological processes such as the ultraviolet-B radiation (UV-B) response and cold tolerance. In this study, 56 genes were identified in upland cotton by searching the associated reference genomes. The genes were found to be unevenly distributed on 26 chromosomes, except A06, A12, D03, and D12. Phylogenetic analysis by maximum-likelihood revealed that the genes were divided into five subgroups. The RCC1 genes within the same group shared similar exon/intron patterns and conserved motifs in their encoded proteins. Most genes of the RCC1 family are expressed differently under various hormone treatments and are negatively controlled by salt stress. Gh_A05G3028 and Gh_D10G2310, which encode two proteins located in the nucleus, were strongly induced under salt treatment, while mutants of their homoeologous gene (UVR8) in Arabidopsis and VIGS (virus induced gene silencing) lines of the two genes above in G. hirsutum exhibited a salt-sensitive phenotype indicating their potential role in salt resistance in cotton. These results provide valuable reference data for further study of RCC1 genes in cotton

Analyses of the sucrose synthase gene family in cotton: structure, phylogeny and expression patterns

Abstract Background In plants, sucrose synthase (Sus) is widely considered as a key enzyme involved in sucrose metabolism. Several paralogous genes encoding different isozymes of Sus have been identified and characterized in multiple plant genomes, while limited information of Sus genes is available to date for cotton. Results Here, we report the molecular cloning, structural organization, phylogenetic evolution and expression profiles of seven Sus genes (GaSus1 to 7) identified from diploid fiber cotton (Gossypium arboreum). Comparisons between cDNA and genomic sequences revealed that the cotton GaSus genes were interrupted by multiple introns. Comparative screening of introns in homologous genes demonstrated that the number and position of Sus introns are highly conserved among Sus genes in cotton and other more distantly related plant species. Phylogenetic analysis showed that GaSus1, GaSus2, GaSus3, GaSus4 and GaSus5 could be clustered together into a dicot Sus group, while GaSus6 and GaSus7 were separated evenly into other two groups, with members from both dicot and monocot species. Expression profiles analyses of the seven Sus genes indicated that except GaSus2, of which the transcripts was undetectable in all tissues examined, and GaSus7, which was only expressed in stem and petal, the other five paralogues were differentially expressed in a wide ranges of tissues, and showed development-dependent expression profiles in cotton fiber cells. Conclusions This is a comprehensive study of the Sus gene family in cotton plant. The results presented in this work provide new insights into the evolutionary conservation and sub-functional divergence of the cotton Sus gene family in response to cotton fiber growth and development.</p

Genetic Mapping and Candidate Gene Prediction of a QTL Related to Early Heading on Wild Emmer Chromosome 7BS in the Genetic Background of Common Wheat

Heading date (HD) is an essential agronomic objective in wheat conventional breeding. Field experiments from several years and locations indicated that the chromosome arm substitution line (CASL) of wild emmer chromosome 7BS in the genetic background of common wheat var. Chinese Spring (CS) always showed a substantially earlier HD than CS planted in different seasons; usually about 8 d earlier than CS grown under a normal autumn sowing season. CASL7BS consistently showed a much earlier HD than CS when treated for vernalization under a long or short photoperiod and then grown under a short or long photoperiod in the growth room. CASL7BS showed faster spike development than CS at the stages before the glume stage when grown under long days, and depicted relatively rapid growth at all stages when grown under short days. To map the early gene in CASL7BS, F2 plants from the cross of CASL7BS and CS were planted in the field and growth room, forming two mapping populations (P1 and P2, respectively). According to the HD distribution of P1, the HD was most likely regulated by a dominant gene. A QTL was detected consistently in the distal region of about 8.94 cM flanked by C268 and C309 with LOD scores of 5–8, explaining 9.14 and 12.35% of the phenotypic variation in the two mapping populations. The QTL was further narrowed down to an interval between ZAFU058724 and ZAFU061354 of 58–61 Mb based on the HD and genotype of F3 and F4 families. A total of 41 genes were located in this region, and eleven of them were thought to be the candidate genes based on the gene functions. According to the HD and mapping location, the QTL identified in this study was a new gene associated with flowering, which will be helpful in understanding the mechanism of wheat flowering and for breeding an early wheat variety

Phase formation and magnetic properties of (Nd1−xYx)14Fe80B6 melt-spun ribbons

Phase formation and magnetic properties of (Nd _1−x Y _x ) _14 Fe _80 B _6 (x = 0.1–0.8) alloys were investigated experimentally by x-ray diffraction (XRD) and vibrating sample magnetometer (VSM). The phase structure analysis reveals that the as-cast (Nd _1−x Y _x ) _14 Fe _80 B _6 alloys were made of 2:14:1 phase with tetragonal Nd _2 Fe _14 B-tpyed structure, REFe _2 and α -Fe phases, while the melt-spun ribbons are composed of 2:14:1 phase and α -Fe Phase. Based on the magnetic measurements, the remanence (B _r ), the coercivity (H _cj ), the maximum magnetic energy product ((BH) _max ) and the Curie temperatures (T _c ) of (Nd _1−x Y _x ) _14 Fe _80 B _6 ribbons reduces gradually with increasing Y substitution. The relatively high coercivity (6.75 kOe) of (Nd _0.4 Y _0.6 ) _14 Fe _80 B _6 ribbon with high Y substitution was achieved, which indicates that good magnetic properties of Nd–Y–Fe–B ribbons would be obtained through the design of alloy composition and phase formation

Mapping of Ppd-B1, a Major Candidate Gene for Late Heading on Wild Emmer Chromosome Arm 2BS and Assessment of Its Interactions with Early Heading QTLs on 3AL.

Wheat heading date is an important agronomic trait determining maturation time and yield. A set of common wheat (Triticum aestivum var. Chinese Spring; CS)-wild emmer (T. turgidum L. subsp. dicoccoides (TDIC)) chromosome arm substitution lines (CASLs) was used to identify and allocate QTLs conferring late or early spike emergence by examining heading date. Genetic loci accelerating heading were found on TDIC chromosome arms 3AL and 7BS, while loci delaying heading were located on 4AL and 2BS. To map QTLs conferring late heading on 2BS, F2 populations derived from two cross combinations of CASL2BS × CS and CASL3AL × CASL2BS were developed and each planted at two times, constituting four F2 mapping populations. Heading date varied continuously among individuals of these four populations, suggesting quantitative characteristics. A genetic map of 2BS, consisting of 23 SSR and one single-stranded conformation polymorphism (SSCP) marker(s), was constructed using these F2 populations. This map spanned a genetic length of 53.2 cM with average marker density of 2.3 cM. The photoperiod-sensitivity gene Ppd-B1 was mapped to chromosome arm 2BS as a SSCP molecular marker, and was validated as tightly linked to a major QTL governing late heading of CASL2BS in all mapping populations. A significant dominance by additive effect of Ppd-B1 with the LUX gene located on 3AL was also detected. CS had more copies of Ppd-B1 than CASL2BS, implying that increased copy number could elevate the expression of Ppd-1 in CS, also increasing expression of LUX and FT genes and causing CS to have an earlier heading date than CASL2BS in long days

Divergence and evolution of cotton bHLH proteins from diploid to allotetraploid

Abstract Background Polyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization. Results We compared the genome sequences of tetraploid cotton (Gossypium hirsutum) and its two diploid progenitors, G. arboreum and G. raimondii, and found that the bHLH genes were conserved over the polyploidization. Oppositely, the expression of the homeolgous gene pairs was diversified. The biased homeologous proportion for bHLH family is significantly higher (64.6%) than the genome wide homeologous expression bias (40%). Compared with cacao (T. cacao), orthologous genes only accounted for a small proportion (41.7%) of whole cotton bHLHs family. The further Ks analysis indicated that bHLH genes underwent at least two distinct episodes of whole genome duplication: a recent duplication (1.0–60.0 million years ago, MYA, 0.005  60.0 MYA, 0.312 < Ks < 3.0). The old duplication event might have played a key role in the expansion of the bHLH family. Both recent and old duplicated pairs (68.8%) showed a divergent expression profile, indicating specialized functions. The expression diversification of the duplicated genes suggested it might be a universal feature of the long-term evolution of cotton. Conclusions Overview of cotton bHLH proteins indicated a conserved and divergent evolution from diploids to allotetraploid. Our results provided an excellent example for studying the long-term evolution of polyploidy

Consensus Genetic Linkage Map Construction Based on One Common Parental Line for QTL Mapping in Wheat

The consensus map is used for the verification of marker order, quantitative trait locus (QTL) mapping and molecular marker-assisted selection (MAS) in wheat breeding. In this study, a wheat consensus genetic map named as Sp7A_G7A, was constructed using 5643 SNP markers in two double haploid (DH) populations of Spitfire × Bethlehem-7AS (Sp7A) and Gregory × Bethlehem-7AS (G7A), covering 4376.70 cM of 21 chromosomes (chr) with an average interval of 0.78 cM. The collinearity of the linkage maps with the consensus map of Con_map_Wang2014 and the physical map of wheat reference genome (IWGSC RefSeq v1.0) were analyzed based on the Spearman rank correlation coefficients. As results, the three constructed genetic maps of Sp7A, G7A and Sp7A_G7A showed high collinearity with the Con_map_Wang2014 and the physical map, and importantly, the collinearity level between our constructed maps and the wheat physical map is higher than that between the Con_map_Wang2014 and the physical map. The seed coat color QTL detected in both populations under multiple environments were on the region (745.73–760.14 Mbp) of the seed color gene R-B1/Tamyb10-B1 (TraesCS3B02G515900, 3B: 757,918,264–757,920,082 bp). The validated consensus map will be beneficial for QTL mapping, positional cloning, meta-QTL analysis and wheat breading

Rate variation among nuclear genes and the age of polyploidy in Gossypium

11 pages, 2 figures, 3 tables.-- PMID: 12679546 [PubMed].-- Full-text paper available Open Access at journal site.Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors, and an outgroup. Substitution rates varied widely among the 48 genes, with silent and replacement substitution levels varying from 0.018 to 0.162 and from 0.000 to 0.073, respectively, in comparisons between orthologous Gossypium and outgroup sequences. However, about 90% of the genes had silent substitution rates spanning a more narrow threefold range. Because there was no evidence of rate heterogeneity among lineages for any gene and because rates were highly correlated in independent tests, evolutionary rate is inferred to be a property of each gene or its genetic milieu rather than the clade to which it belongs. Evidence from approximately 200,000 nucleotides (40,000 per genome) suggests that polyploidy in Gossypium led to a modest enhancement in rates of nucleotide substitution. Phylogenetic analysis for each gene yielded the topology expected from organismal history, indicating an absence of gene conversion or recombination among homoeologs subsequent to allopolyploid formation. Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA.Financial support was provided by the National Science Foundation, the US-Israel Binational Science Foundation, the Plant Sciences Institute of Iowa State University, and the Spanish Ministry of Education, Culture and Sports.Peer reviewe