QTL Mapping And Transcriptome Analysis For Fiber Quality Traits In A Set Of Gossypium Mustelinum Introgression Lines

Cotton?Gossypium L.?is one of the most important crops in the world.Cotton fiber is also the most important natural fiber in the textile industry,and the majority production of cotton fiber is from Gossypium hirsutum.The innovation of modern textile technology and the general increase of consumers' demand put forward higher requirements on cotton fiber quality in China.However,some disadvantages exist in Chinese cotton fiber,e.g.low fiber strength and improporate combination of fiber length and strength.Consequently,it is urgent for us to improve the quality of cotton fiber.In this study,sixty-five G.mustelinum introgression lines?ILs?with G.hirsutum PD94042 as background were genotyped and fiber quality traits were collected in three environments.QTLs of fiber quality traits were mapped,and QTL-based near-isogenic lines were selected,including IL9,an IL with elite fiber strength and length.In order to identify candidate genes related with fiber quality traits,we conducted fiber transcriptome analysis with PD94042 and IL9 at two development periods of 17 dpa and 21 dpa.The conclusions were as follows:?1?More than 2000 pairs of primers were applied for polymorphism screening in the two parents,PD94042 and G.mustelinum,and a total of 379 polymorphic loci were identified.?2?The phenotypic analyses showed that fiber strength,fiber length and elongation of the ILs followed normal distribution and the three traits of most ILs were better than that of the G.hirsutum parent PD94042.Fiber uniformity and Micronaire of the ILs did not follow normal distribution,but there was also part of ILs with better traits than PD94042.?3?The genome position of the polymorphic loci was identified based on the whole-genome sequences of G.hirsutum.Based on this information,a genetic linkage map was constructed using the 379 SSR loci with the mapping software Map Maker 3.0.The map covers 26 chromosomes,including 355 molecular markers distributed on 30 linkage groups with total distance of 2551.4 c M,which is about 51 percentege of the cotton genome.?4?Win QTLCart 2.5 was used for QTL mapping.A total of 132 QTLs were detected,including 28 QTLs related to fiber length,30 QTLs related to fiber strength,32 QTLs related to Micronaire,20 QTLs related to fiber uniformity,23 QTLs related to fiber elongation.Two stable QTLs?q UHM-1-1 and q UHM-22-1?were identified.?5?Two sets of QTL-based near isogenic lines were constructed based on the fiber length QTL?q UHM-1-1?q UHM-22-1?respectively,with one set including IL6,IL9,IL15,and IL17,and the other set including IL6,IL9,IL11,and IL17.One elite IL?IL9?was selected as a near isogenic line of G.hirsutum parent PD94042,and these two near isogenic lines were used for further transcriptome analysis.?6?The scatter diagram was used for DEGs in four kinds of samples.Totally 1112 DEGs are up regulated and 820 DEGs are down regulated in IL9-17dpa-VS-IL9-21dpa;1098 DEGs are up regulated and 988 DEGs are down regulated in PD-17dpa-VS-PD-21dpa;299 DEGs are up regulated and 142 DEGs are down regulated in PD-17dpa-VS-IL9-17dpa;147 DEGs are up regulated and 64 DEGs are down regulated in PD-21dpa-VS-IL9-21 dpa.?7?Gene Ontology?GO?enrichment analysis of the annotated DEGs showed that these DEGs are rich in two main biological processes?cellular process and metabolic process?and two main molecular functions?binding and catalytic activity?.KEGG pathway analysis showed that these DEGs are mainly enriched in metabolic pathways and biosynthesis of secondary metabolites.?8?A total of 46 DEGs were chosen for the candidate genes by comparing PD94042 and IL9 because of the specialty of the materials,and the results of q RT-PCR analysis for 12 selected DEGs were consistent with that of transcriptome analysis.Five genes are likely to be related with the process of fiber development,whose gene numbers are Cot AD₀4694,Cot AD₄4496,Cot AD₅6281,Cot AD₂0689 and Cot AD₆5308,coding ferredoxin?FD?,GDSL esterase/lipase,calcium-binding protein CML49,leucine-rich repeat receptor-like protein?LRR-RLK?and LRR receptor-like serine/threonine-protein kinase GSO2,respectively.?9?Toyally 6 DEGs were found on the genetic linkage map by compairing the location of tested DEGs and molecular markers,including the gene coding stress protein?Cot AD₆8165?,which is located between CICR186-DPL0241 on Chromosome 5;the gene coding calcium-binding protein CML49?Cot AD₅6281?,which is located between CICR306-DPL0646 on Chromosome 8;genes coding ran-binding protein?Cot AD₂5133?and GDSL esterase/lipase?Cot AD₄4496?,which are both located between MUB1035a-DPL0507 on Chromosome 9;genes coding leucine-rich repeat receptor-like protein kinase?Cot AD₂0689?and lupeol synthase-like?Cot AD₂4472?,which are both located between CICR836-BNL3563 on Chromosome 10.More markers within these regions will be used to screen the IL population,so as to identify more fiber quality QTLs and the potential candidate genes.