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Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood, both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors (GhERF1s), anchored on Chr‐A07 and Chr‐D07, were isolated from a high‐yielding cotton hybrid (XZM2) and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress. Nucleotide sequence analysis of 524 diverse accessions, together with quantitative real‐time polymerase chain reaction analysis, elucidated that de‐functionalization of GhERF1‐7A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1‐7A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1‐7A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo‐functionalization of GhERF1‐7A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high‐yielding cotton cultivars. Both de‐ and neo‐functionalization occurred in one of the duplicate genes, thus providing new genomic insight into the evolution of allotetraploid cotton species. Whole genome duplication usually results in massive genome restructuring. We report both de‐ and neo‐functionalization occurred in duplicate ethylene responsive factors of B3 subgroup of ERF subfamily, which involved in abiotic stress tolerance after the formation of allotetraploid cotton. Our finding provides a new genomic insight into the evolution of allotetraploid species. [ABSTRACT FROM AUTHOR]

A bacterial artificial chromosome (BAC) library was constructed for Gossypium hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384− well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carried out by four-round polymerase chain reactions using 23 simple sequence repeats (SSR) markers, three sequence-related amplified polymorphism markers and one pair of primers for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 (A12) and 26 (D12) according to the genetic map, these BAC clones are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with important agronomic traits. [ABSTRACT FROM AUTHOR]

Summary: Cotton cultivars have evolved to produce extensive, long, seed‐born fibers important for the textile industry, but we know little about the molecular mechanism underlying spinnable fiber formation. Here, we report how PACLOBUTRAZOL RESISTANCE 1 (PRE1) in cotton, which encodes a basic helix‐loop‐helix (bHLH) transcription factor, is a target gene of spinnable fiber evolution. Differential expression of homoeologous genes in polyploids is thought to be important to plant adaptation and novel phenotypes. PRE1 expression is specific to cotton fiber cells, upregulated during their rapid elongation stage and A‐homoeologous biased in allotetraploid cultivars. Transgenic studies demonstrated that PRE1 is a positive regulator of fiber elongation. We determined that the natural variation of the canonical TATA‐box, a regulatory element commonly found in many eukaryotic core promoters, is necessary for subgenome‐biased PRE1 expression, representing a mechanism underlying the selection of homoeologous genes. Thus, variations in the promoter of the cell elongation regulator gene PRE1 have contributed to spinnable fiber formation in cotton. Overexpression of GhPRE1 in transgenic cotton yields longer fibers with improved quality parameters, indicating that this bHLH gene is useful for improving cotton fiber quality. [ABSTRACT FROM AUTHOR]

Bamboo occupies an important phylogenetic node in the grass family and plays a significant role in the forest industry. We produced 1.2 Mb of tetraploid moso bamboo (Phyllostachys pubescens E. Mazel ex H. de Leh.) sequences from 13 bacterial artificial chromosome (BAC) clones, and these are the largest genomic sequences available so far from the subfamily Bambusoideae. The content of repetitive elements (36.2%) in bamboo is similar to that in rice. Both rice and sorghum exhibit high genomic synteny with bamboo, which suggests that rice and sorghum may be useful as models for decoding Bambusoideae genomes. [ABSTRACT FROM AUTHOR]

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 F2 plants derived from the cross of two Asiatic cotton cultivars ( Gossypium arboreum L.) Jianglingzhongmian × 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 F2 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) ≥ 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 At and Dt 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. [ABSTRACT FROM AUTHOR]

To identify alien chromosomes in recipient progenies and to analyze genome components in polyploidy, a genomic in situ hybridization (GISH) technique that is suitable for cotton was developed using increased stringency conditions. The increased stringency conditions were a combination of the four factors in the following optimized state: 100:1 ratio of blocking DNA to probe, 60% formamide wash solution, 43 °C temperature wash and a 13 min wash. Under these specific conditions using gDNA from Gossypium sturtianum (C1C1) as a probe, strong hybridization signals were only observed on chromosomes from the C1 genome in somatic cells of the hybrid F1 ( G. hirsutum × G. sturtianum) (AtDtC1). Therefore, GISH was able to discriminate parental chromosomes in the hybrid. Further, we developed a multi-color GISH to simultaneously discriminate the three genomes of the above hybrid. The results repeatedly displayed the three genomes, At, Dt, and C1, and each set of chromosomes with a unique color, making them easy to identify. The power of the multi-color GISH was proven by analysis of the hexaploid hybrid F1 ( G. hirsutum × G. australe) (AtAtDtDtG2G2). We believe that the powerful multi-color GISH technique could be applied extensively to analyze the genome component in polyploidy and to identify alien chromosomes in the recipient progenies. [ABSTRACT FROM AUTHOR]