Dajun Liu

Integrated mapping and characterization of the gene underlying the okra leaf trait in Gossypium hirsutum L

Highlight Characterization of GhOKRA suggests the involvement of protein activity and transcription of GhOKRA in regulating cotton leaf shape and a possible origin of the okra leaf trait by gene conversion.

Fine-mapping qFS07.1 controlling fiber strength in upland cotton (Gossypium hirsutum L.)

Key messageqFS07.1 controlling fiber strength was fine-mapped to a 62.6-kb region containing four annotated genes. RT-qPCR and sequence of candidate genes identified an LRR RLK gene as the most likely candidate.AbstractFiber strength is an important component of cotton fiber quality and is associated with other properties, such as fiber maturity, fineness, and length. Stable QTL qFS07.1, controlling fiber strength, had been identified on chromosome 7 in an upland cotton recombinant inbred line (RIL) population from a cross (CCRI35 × Yumian1) described in our previous studies. To fine-map qFS07.1, an F2 population with 2484 individual plants from a cross between recombinant line RIL014 and CCRI35 was established. A total of 1518 SSR primer pairs, including 1062, designed from chromosome 1 of the Gossypium raimondii genome and 456 from chromosome 1 of the G. arboreum genome (corresponding to the QTL region) were used to fine-map qFS07.1, and qFS07.1 was mapped into a 62.6-kb genome region which contained four annotated genes on chromosome A07 of G. hirsutum. RT-qPCR and comparative analysis of candidate genes revealed a leucine-rich repeat protein kinase (LRR RLK) family protein to be a promising candidate gene for qFS07.1. Fine mapping and identification of the candidate gene for qFS07.1 will play a vital role in marker-assisted selection (MAS) and the study of mechanism of cotton fiber development.

Genetic Map Construction and Fiber Quality QTL Mapping Using the CottonSNP80K Array in Upland Cotton

Cotton fiber quality traits are controlled by multiple quantitative trait loci (QTL), and the improvement of these traits requires extensive germplasm. Herein, an Upland cotton cultivar from America, Acala Maxxa, was crossed with a local high fiber quality cultivar, Yumian 1, and 180 recombinant inbred lines (RILs) were obtained. In order to dissect the genetic basis of fiber quality differences between these parents, a genetic map containing 12116 SNP markers was constructed using the CottonSNP80K assay, which covered 3741.81 cM with an average distance of 0.31 cM between markers. Based on the genetic map and growouts in three environments, we detected a total of 104 QTL controlling fiber quality traits. Among these QTL, 25 were detected in all three environments and 35 in two environments. Meanwhile, 19 QTL clusters were also identified, and nine contained at least one stable QTL (detected in three environments for a given trait). These stable QTL or QTL clusters are priorities for fine mapping, identifying candidate genes, elaborating molecular mechanisms of fiber development, and application in cotton breeding programs by marker-assisted selection (MAS).

Chromosome structural variation of two cultivated tetraploid cottons and their ancestral diploid species based on a new high-density genetic map

A high-resolution genetic map is a useful tool for assaying genomic structural variation and clarifying the evolution of polyploid cotton. A total of 36956 SSRs, including 11289 released in previous studies and 25567 which were newly developed based on the genome sequences of G. arboreum and G. raimondii, were utilized to construct a new genetic map. The new high-density genetic map includes 6009 loci and spanned 3863.97 cM with an average distance of 0.64 cM between consecutive markers. Four inversions (one between Chr08 and Chr24, one between Chr09 and Chr23 and two between Chr10 and Chr20) were identified by homology analysis. Comparative genomic analysis between genetic map and two diploid cottons showed that structural variations between the A genome and At subgenome are more extensive than between D genome and Dt subgenome. A total of 17 inversions, seven simple translocations and two reciprocal translocations were identified between genetic map and G. raimondii. Good colinearity was revealed between the corresponding chromosomes of tetraploid G. hirsutum and G. barbadense genomes, but a total of 16 inversions were detected between them. These results will accelerate the process of evolution analysis of Gossipium genus.