A targeted QTL analysis for fiber length using a genetic population between two introgressed backcrossed inbred lines in upland cotton(Gossypium hirsutum)

Cotton fiber is the most important natural raw material for the textile industry, and fiber length(FL) is one of the most important traits in cotton.Quantitative trait locus(QTL)mapping based on high-density genetic maps is an efficient approach to identify genetic regions for FL.In our study, two backcrossed inbred lines(BILs) were chosen as parents to construct a high-density genetic map in F2 which was used to fine map FL QTL in F2:3 population.The genetic map had a total size of 3462.8 cM, containing 9182 singlenucleotide polymorphisms(SNPs) based on genotyping-by-sequencing.Two FL related stable QTL were identified on two chromosomes(qFL-A08–1 on A08 and qFL-D03–1 on D03),and qFL-A08–1 was confirmed by a meta-analysis.Utilizing previously obtained RNA-seq data for the two BILs and qRT-PCR analysis, two candidate genes annotated as cytochrome b5(CB5, Gh_A08 G1729) and microtubule end-binding 1 C(EB1C, Gh_D03 G0232) that may regulate FL during the fiber elongation stage were identified.In addition, nine recombination hotspots in this population were found.The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of fiber elongation.

A comparative analysis of small RNAs between two Upland cotton backcross inbred lines with different fiber length: Expression and distribution

The cotton fiber is the most important raw material for the textile industry and an ideal model system for studying cell elongation. However, the genetic variation of fiber elongation in relation to miRNA is poorly understood. A high-throughput comparative RNA-seq of two lines differing in fiber length(FL) from a backcross inbred line(BIL)population of G. hirsutum × G. barbadense revealed differentially expressed(DE) miRNAs and their targets in rapidly elongating fibers. A real-time quantitative PCR analysis was further performed to validate the results. A total of 463(including 47 DE) miRNAs were identified,and seven DE miRNAs were co-localized with seven FL quantitative trait loci(QTL)identified in the G. hirsutum × G. barbadense population. Of 82(including 21 DE) targets identified, nine(including one DE) were also co-localized with the seven FL QTL. The relationship between the allopolyploid and its diploid ancestral species with respect to miRNAs and their targets was also characterized. These results will facilitate the understanding of the molecular genetic mechanism of fiber elongation with regards to miRNAs in cotton.

High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

A high-density linkage map was constructed for an F2 population derived from an Interspecific cross of cultivated allotetraploid species between Gossypium hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the Interspecific cross of ＂CRI 36 × Hal 7124＂ were genotyped at I 252 polymorphic loci Including a novel marker system, target region amplification polymorphism （TRAP）. The map consists of 1 097 markers, including 697 simple se- quence repeats （SSRs）, 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were Identified In tetraploid cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

Molecular Cloning and Function Analysis of Two SQUAMOSA-Like MADS-Box Genes From Gossypium hirsutum L.

The MADS-box genes encode a large family of transcription factors having diverse roles in plant development. The SQUAMOSA （SQUA）/APETALA1 （AP1）/FRUITFULL （FUL） subfamily genes are essential regulators of floral transition and floral organ identity. Here we cloned two MADS-box genes, GhMADS22 and GhMADS23, belonging to the SQUA/AP1/FUL subgroup from Gossypium hirsutum L. Phylogenetic analysis and sequence alignment showed that GhMAD$22 and GhMADS23 belonged to the euFUL and euAP1 subclades, respectively. The two genes both had eight exons and seven introns from the start codon to the stop codon according to the alignment between the obtained cDNA sequence and the Gossypium raimondii L. genome sequence. Expression profile analysis showed that GhMADS22 and GhMADS23 were highly expressed in developing shoot apices, bracts, and sepals. Gibberellic acid promoted GhMADS22 and GhMADS23 expression in the shoot apex. Transgenic Arabidopsis lines overexpressing 35S：：GhMADS22 had abnormal flowers and bolted earlier than wild type under long-day conditions （16 h light/8 h dark）. Moreover, GhMADS22 over- expression delayed floral organ senescence and abscission and it could also respond to abscisic acid. In summary, GhMADS22 may have functions in promoting flowering, improving resistance and delaying senescence for cotton and thus it may be a candidate target for promoting early-maturation in cotton breeding.

Selection and Characterization of a Novel Photoperiod-Sensitive Male Sterile Line in Upland Cotton

Upland cotton （Gossypium hirsutum L.） shows strong heterosis. However, heterosis is not widely utilized owing to the high cost of hybrid seed production. Creation of a photoperiod-sensitive genetic male sterile line could substantially reduce the cost of hybrid seed production in upland cotton. Such a mutant with virescent marker was found by space mutation in near-earth orbit and its traits had been stable after 4 years of selection in Anyang and Sanya, China. This mutant was fertile with an 11-12.5 h photoperiod when the temperature was higher than 21.5 ℃ and was sterile with a 13-14.5 h photoperiod. Genetic analysis indicated that both traits were controlled by a single recessive gene or two closely linked genes. Also, the cytological observations and transcriptome profiling analysis showed that the degradation of pollen grain cytoplasm should be the primary reason why the mutant line were male sterile under long-day conditions.

Identification and Profiling of Known and Novel Fiber MicroRNAs during the Secondary Wall Thickening Stage in Cotton(Gossypium hirsutum) via High-Throughput Sequencing

Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992）. Cotton fibers are single-celled trichomes that emerge from the ovule epidermal cells. Indexed by the number of days post-anthesis （dpa）, fiber morphogenesis includes four distinct but overlapping steps： initiation （0-3 dpa）, elongation （3-20 dpa）, secondary cell wall thickening （15-45 dpa） and maturation （40-60 dpa） （Yang et al., 2008, Du et al., 2013）. The efficiency and duration of each morphogenesis stage is important to the quality attributes of the mature fiber. Cell elongation is critical for fiber length, whereas secondary cell wall thickening is important for fiber fineness and strength （Meinert and Delmer, 1977）.