Zhengsheng Zhang

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).

Developing Exon-Targeted Intron-Exon Splicing Junction Marker and Establishing Genetic Map of Upland Cotton

Abstract The objective of this study was to develop new molecular markers and locate them into the existing genetic map of upland cotton ( Gossypium hirsutum L.). Exon-targeted intron-exon splice junction (ET-ISJ) maker primers were designed according to the conserved sequences of intron-exon splicing junction. A total of 1280 ET-ISJ primer combinations were used to screen polymorphism between upland cotton cultivars Yumian 1 and T586. Sixty-nine primer combinations were polymorphic, which accounted for 5.4% of the total primer combinations. A mapping population of F 2:7 from Yumian 1 × T586 were tested using the 69 ET-ISJ markers, and 70 ET-ISJ loci were obtained. Linkage analysis was conducted using the 70 ET-ISJ loci as well as 523 simple sequence repeat (SSR), 59 intron-tageted intron-exon splice junction (IT-ISJ), 29 sequence-related amplified polymorphism (SRAP), and 8 morphological loci. The linkage map obtained was composed of 59 linkage groups and 673 loci including 68 ET-ISJ, 510 SSR, 58 IT-ISJ, 29 SRAP, and 8 morphological loci. This linkage map covered 3216.7 cM (72.3%) of cotton genome with an average interval of 4.8 cM between 2 adjacent markers. Sixty-eight ET-ISJ loci were located on 20 chromosomes. The present study showed that ET-ISJ markers are relatively stable, highly polymorphic, and effective in constructing genetic map of upland cotton.

Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers

Lycium barbarum, commonly known as goji, is important in Chinese herbal medicine and its fruit is a very important agricultural and biological product. However, the molecular mechanism of formation of its fruit and associated medicinal and nutritional components is unexplored. Moreover, this species lacks SSR markers due to lack of genomic and transcriptomic information. In this study, a total of 139,333 unigenes with average length of 1049 bp and N50 of 1579 bp are obtained by trinity assembly from Illumina sequencing reads. A total of 92,498 (66.38%) unigenes showed similarities in at least one database including Nr (46.15%), Nt (56.56%), KO (15.56%), Swiss-prot (33.34%), Pfam (33.43%), GO (33.62%) and KOG/COG (17.55%). Genes in flavonoid and taurine biosynthesis pathways were found and validated by RT-qPCR. A total of 50,093 EST-SSRs were identified from 38,922 unigenes, and 22,537 EST-SSR primer pairs were designed. Four hundred pairs of SSR markers were randomly selected to validate assembly quality, of which 352 (88%) were successful in PCR amplification of genomic DNA from 11 Lycium accessions and 210 produced polymorphisms. The polymorphic loci showed that the genetic similarity of the 11 Lycium accessions ranged from 0.50 to 0.99 and the accessions could be divided into 4 groups. These results will facilitate investigations of the molecular mechanism of formation of L. barbarum fruit and associated medicinal and nutritional components, and will be of value to novel gene discovery and functional genomic studies. The EST-SSR markers will be useful for genetic diversity evaluation, genetic mapping and marker-assisted breeding.

Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations

Advanced backcross populations improve detection of small‐effect QTL Both cultivated tetraploid Gossypium species have favorable and unfavorable alleles Clustering of different trait QTL were variable in reciprocal backgrounds Three stable and four reciprocal QTL were identified in reciprocal backgrounds

A D-genome-originated Ty1/ Copia -type retrotransposon family expanded significantly in tetraploid cottons

Retrotransposons comprise of a major fraction of higher plant genomes, and their proliferation and elimination have profound effects on genome evolution and gene functions as well. Previously we found a D-genome-originated Ty1/Copia-type LTR (DOCL) retrotransposon in the chromosome A08 of upland cotton. To further characterize the DOCL retrotransposon family, a total of 342 DOCL retrotransposons were identified in the sequenced cotton genomes, including 73, 157, and 112 from Gossypium raimondii, G. hirsutum, and G. barbadense, respectively. According to phylogenetic analysis, the DOCL family was divided into nine groups (G1–G9), among which five groups (G1–G4 and G9, including 292 members) were proliferated after the formation of tetraploid cottons. It was found that the majority of DOCL retrotransposons (especially those in G2, G3 and G9) inserted in non-allelic loci in G. hirsutum and G. barbadense, suggesting that their proliferations were relatively independent in different tetraploid cottons. Furthermore, DOCL retrotransposons inserted in coding regions largely eliminated expression of the targeted genes in G. hirsutum or G. barbadense. Our data suggested that recent proliferation of retrotransposon families like DOCL was one of important evolutionary forces driving diversification and evolution of tetraploid cottons.

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.

Comparative genetic variation of fiber quality traits in reciprocal advanced backcross populations

Introgressive breeding to introduce both obvious variation into a gene pool, and to unmask cryptic variation masked by close linkage or epistatic interactions, has repeatedly been attempted to improve fiber traits in Gossypium hirsutum by employing Gossypium barbadense as a donor parent. This study reports genetic variation for fiber quality traits in reciprocal advanced backcross populations between G. hirsutum cultivar Acala Maxxa and G. barbadense cultivar Pima S6. Micronaire (MIC), elongation (ELO), strength (STR), upper half mean length (UHM), and uniformity index (UI) showed significant genotypic variance, albeit different in the respective backgrounds for all traits except UI. Different levels of variation among genotypes for the same traits in reciprocal backgrounds suggest different levels of epistatic interactions, a hypothesis supported by a significant difference in transgressive segregants in Acala Maxxa and Pima S6 backgrounds. In Acala Maxxa background, 18, 18, 7, and 3 genotypes had significantly better MIC, ELO, STR and UHM, respectively, than Acala Maxxa. In Pima S6 background 10, 5, 8, and 11 genotypes had significantly better MIC, ELO, STR, and UHM, respectively, than Pima S6. Increased genetic variation and improved fiber quality in both backgrounds appears attainable using reciprocal introgression; however, the number of genotypes with simultaneous improvement for multiple fiber quality traits was higher in Acala Maxxa than Pima S6 background. Reciprocal populations provide a platform to study cytoplasmic effects on genetic variation and heritability of fiber quality traits, and estimate the size of base populations required to obtain genotypes with genetic gain by backcross breeding.