Baoliang Zhou

Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

Development and molecular cytogenetic analysis of wheat-Haynaldia villosa 6VS/6AL translocation lines specifying resistance to powdery mildew

Several Triticum aestivum L.-Haynaldia villosa disomic 6VS/6AL translocation lines with powdery mildew resistance were developed from the hybridization between common wheat cultivar Yangmai 5 and alien substitution line 6V(6A). Mitotic and meiotic C-banding analysis, aneuploid analysis with double ditelosomic stocks, in situ hybridization, as well as the phenotypic assessment of powdery mildew resistance, were used to characterize these lines. The same translocated chromosome, with breakpoints near the centromere, appears to be present in all the lines, despite variation among the lines in their morphology and agronomic characteristics. The resistance gene, conferred by H. villosa and designated as Pm21, is a new and promising source of powdery mildew resistance in wheat breeding.

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites

Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11–20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium

Diploid species with a common Gossypium origin are highly diverse in morphology and have been classified into eight genomic groups designated A–G and K. In this study, the transferability of 207 Gossypium arboreum-derived expressed sequence tag-simple sequence repeat (EST-SSR) primer pairs was examined among 25 different diploid accessions representing 7 genomes and 23 Gossypium species. We found that 124 of the 207 (60%) primer pairs produced amplification products in all 25 accessions. The remaining 83 (40%) primer pairs produced amplification in only a subset of species, ranging from 13 to 22 species, which is consistent with some genome- and species-specific amplification. The cross-species amplification of these EST-SSRs in 22 diploid species was 96.5% in 4,554 combinations (207 SSRs×22 species), indicative of a high transferability among the Gossypium species. Furthermore, a high level of polymorphism with an average number of 6.53 alleles per SSR marker was detected. No correlation was found between the repeat motif type and cross-species amplification. DNA sequencing showed that the high-level polymorphism findings was mainly due to changes in the number of repeat motifs and that the high transferability can be attributed to a higher-level conservation in the flanking regions among these diploid Gossypium species. The transferability among these different diploid species presented here can increase the efficiency of transferring genetic information across species and further enhance their introgression into cultivated cotton species by the molecular tagging of important genes existing in these diploid species using the EST-SSR markers.

Completely Distinguishing Individual A-Genome Chromosomes and Their Karyotyping Analysis by Multiple Bacterial Artificial Chromosome–Fluorescence in Situ Hybridization

Twenty bacterial artificial chromosome (BAC) clones that could produce bright signals and no or very low fluorescence in situ hybridization (FISH) background were identified from Gossypium arboreum cv. JLZM, and G. hirsutum accession (acc.) TM-1 and 0-613-2R. Combining with 45S and 5S rDNA, a 22-probe cocktail that could identify all 13 G. arboreum chromosomes simultaneously was developed. According to their homology with tetraploid cotton, the G. arboreum chromosomes were designated as A1–A13, and a standard karyotype analysis of G. arboreum was presented. These results demonstrated an application for multiple BAC–FISH in cotton cytogenetic studies and a technique to overcome the problem of simultaneous chromosome recognition in mitotic cotton cells.

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world. The overall genetic diversity among cultivated species of cotton and the genetic changes that occurred during their improvement are poorly understood. Here we report a comprehensive genomic assessment of modern improved upland cotton based on the genome-wide resequencing of 318 landraces and modern improved cultivars or lines. We detected more associated loci for lint yield than for fiber quality, which suggests that lint yield has stronger selection signatures than other traits. We found that two ethylene-pathway-related genes were associated with increased lint yield in improved cultivars. We evaluated the population frequency of each elite allele in historically released cultivar groups and found that 54.8% of the elite genome-wide association study (GWAS) alleles detected were transferred from three founder landraces: Deltapine 15, Stoneville 2B and Uganda Mian. Our results provide a genomic basis for improving cotton cultivars and for further evolutionary analysis of polyploid crops.

MicroRNA expression profiles of porcine skeletal muscle.

MicroRNAs (miRNAs) are endogenous non-coding RNAs of ∼22 nucleotides in length that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. To evaluate the roles of miRNA in porcine skeletal muscle, miRNA expression profiles were investigated using longissimus muscle tissue from pigs at embryonic day 90 (E90) and postpartum day 120 (PD120). First, we used previously known miRNA sequences from humans and mice to perform blast searches against the porcine expressed sequence tag (EST) database; 98 new miRNA candidates were identified according to a range of filtering criteria. These miRNA candidates and 73 known miRNAs (miRBase 13.0) from pigs were chosen for porcine miRNA microarray analysis. A total of 16 newly identified miRNAs and 31 previously known miRNAs were detected in porcine skeletal muscle tissues. During later foetal development at E90, miR-1826, miR-26a, miR-199b and let-7 were highly expressed, whilst miR-1a, miR-133a, miR-26a and miR-1826 showed highest abundance during the fast growing stage at PD120. Using the 47 miRNAs detected by the microarray assay, we performed further investigations using the publicly available porcine mRNA database from NCBI and computed potential target hits using the software rnahybrid. This study identified 16 new miRNA candidates, computed potential target hits for 18 miRNA families and determined the miRNA expression profiles in porcine skeletal muscle tissues at different developmental stages. These results provide a valuable resource for investigators interested in post-transcriptional gene regulation in pigs and related animals.

Simple Sequence Repeat Genetic Linkage Maps of A-genome Diploid Cotton （Gossypium arboreum）

This study introduces the construction of the first intraspecific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat (SSR) markers using 189 F(2) plants derived from the cross of two Asiatic cotton cultivars (Gossypium arboreum L.) Jianglingzhongmian x Zhejiangxiaoshanlüshu. Polymorphisms between the two parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR primers with better polymorphisms were picked out to analyze the F(2) population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, including three phenotypic traits were mapped at a logarithms of odds ratio (LOD) > or = 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the A(t) and D(t) sub-genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.

Genetic basis for glandular trichome formation in cotton

Trichomes originate from epidermal cells and can be classified as either glandular or non-glandular. Gossypium species are characterized by the presence of small and darkly pigmented lysigenous glands that contain large amounts of gossypol. Here, using a dominant glandless mutant, we characterize GoPGF, which encodes a basic helix-loop-helix domain-containing transcription factor, that we propose is a positive regulator of gland formation. Silencing GoPGF leads to a completely glandless phenotype. A single nucleotide insertion in GoPGF, introducing a premature stop codon is found in the duplicate recessive glandless mutant (gl2gl3). The characterization of GoPGF helps to unravel the regulatory network of glandular structure biogenesis, and has implications for understanding the production of secondary metabolites in glands. It also provides a potential molecular basis to generate glandless seed and glanded cotton to not only supply fibre and oil but also provide a source of protein for human consumption.

Molecular cytogenetic characterization of Roegneria ciliaris chromosome additions in common wheat

Abstract The development of alien addition lines is important both for transferring useful genes from related species into common wheat and for studying the relationship between alien chromosomes and those of wheat. Roegneria ciliaris (2n=4x=28, ScScYcYc) is reported to be a potential source of resistance to wheat scab, which may be useful in wheat improvement. The amphiploid common wheat-R. ciliaris and BC1F7 or BC2F6 derivatives were screened by C-banding, genomic in situ hybridization (GISH), fluorescent in situ hybridization (FISH) and restriction fragment length polymorphism (RFLP) for the presence of R. ciliaris chromatin introgressed into wheat. Six lines were identified as disomic chromosome additions (DA), one as a ditelosomic addition (Dt), two as double disomic additions (dDA) and one as a monosomic chromosome addition (MA). RFLP analysis using wheat homoeologous group-specific clones indicated that the R. ciliaris chromosomes involved in these lines belong to groups 1, 2, 3, 5 and 7. The genomic affinities of the added R. ciliaris chromosomes were determined by FISH analysis using the repetitive sequence pCbTaq4.14 as a probe. These data suggest that the R. ciliaris chromosomes in five lines belong to the Sc genome. Based on the molecular cytogenetic data, the lines are designated as DA2Sc#1, Dt2Sc#1L, DA3Sc#1, dDA1Sc#2+5Yc#1, DA5Yc#1, DA7Sc#1, DA7Yc#1 and MA?Yc#1. Based on the present and previous work, 8 of the 14 chromosomes of R. ciliaris have been transferred into wheat.