Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

Repression of microRNA 160 results in retarded seed integument growth and smaller final seed size in cotton

microRNA 160(miR160),targeting auxin response factors(ARFs),plays many roles in plant development.We investigated the role of the mi R160/ARF axis in regulation of cotton seed size.Suppressing mi R160 activity,specifically in the seed coat,led to smaller seeds and less fiber production owing to attenuated growth of the maternal integument.Scanning electron microscopy and histology showed that expansion of cells in the integument was retarded in mi R160-suppressed lines.Four Gh ARF genes were targeted by mi R160 and were upregulated in mi R160-suppressed lines,indicating that a mi R160/ARF axis is present in cotton.Five genes(Ghir_A05 G003740,Scaffold1878 G000010,Ghir_D09 G024980,Ghir_A11 G010730,and Ghir_A05 G041590),associated with reduced seed development were downregulated in mi R160-suppressed lines.Our results suggest that the mi R160/ARF axis controls maternal integument growth to influence seed size by directly or indirectly regulating seed development-associated genes.

The laccase gene Gh Lac1 modulates fiber initiation and elongation by coordinating jasmonic acid and flavonoid metabolism

Cotton fibers are single cells originating in the epidermis of cotton ovules,and serve as the largest natural fiber source for the textile industry.In theory,all epidermal cells have the potential to develop into fibers,but only 15%–25%of epidermis cells develop into commercially viable lint fibers.We previously showed that Gh Lac1 participates in cotton defense against biotic stress.Here we report that Gh Lac1 also has a role in cotton fiber development.Gh Lac1 RNAi lines in cotton showed increased differentiation of fiber initials from epidermis and shortened fiber length,resulting in unchanged lint percentage.Suppression of Gh Lac1 expression led to constitutively hyperaccumulated jasmonic acid(JA)and flavonoids in ovules and fiber cells.In vitro ovule culture experiments confirmed the distinct roles of JA and flavonoids in fiber initiation and elongation,and showed that fiber development is spatially regulated by these chemicals:the increased fiber initiation in Gh Lac1 RNAi lines is caused by hyperaccumulated JA and rutin content during the fiber initiation stage and shortened fiber length is caused by constitutively increased JA and naringenin content during the fiber elongation stage.

Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton

Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.

Evaluation of GOFP over four forest plots using RAMI and UAV measurements

Comparison and validation of canopy reflectance(CR)models are two important steps to ensure their reliability.Pure forest plantations are an ideal type of forest for validating CR models because of their simple background and the low variance in the crown structures which are usually assumed to be identical in most CR models.A Geometric Optical Model for Forest Plantations(GOFP)was compared using dataset in two radiation transfer model intercomparison exercise(RAMI)stands and validated using in situ dataset of detailed optical and structural data of two forest plantations in the Saihanba Forestry Center,China.The results show that(1)the tree distributions in stands described by the hypergeometric model in GOFP show good consistencies with the dataset in the two RAMI stands and measurements from the two Saihanba forest stands;and(2)the CRs simulated with GOFP are also compared well in the two RAMI stands and validated with measurements collected with unmanned aerial vehicles in the two Saihanba stands.GOFP shows a better consistency with the CR measurements than those from CR models for natual forestsbecause the tree distribution in forest plantations is described more reasonably in GOFP.