Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage.

KEY MESSAGE: Genetic variation in a G. barbadense population was revealed using resquencing. GWAS on G.barbadense population identified several candidate genes associated with fiber strength and lint percentage. Gossypium barbadense is the second-largest cultivated cotton species planted in the world, which is characterized by high fiber quality. Here, we described the global pattern of genetic polymorphisms for 240 G. barbadense accessions based on the whole-genome resequencing. A total of 3,632,231 qualified single-nucleotide polymorphisms (SNPs) and 221,354 insertion-deletions (indels) were obtained. We conducted a genome-wide association study (GWAS) on 12 traits under four environments. Two traits with more stable associated variants, fiber strength and lint percentage, were chosen for further analysis. Three putative candidate genes, HD16 orthology (GB_D11G3437), WDL2 orthology (GB_D11G3460) and TUBA1 orthology (GB_D11G3471), on chromosome D11 were found to be associated with fiber strength, and one gene orthologous to Arabidopsis Receptor-like protein kinase HERK 1 (GB_A07G1034) was predicated to be the candidate gene for the lint percentage improvement. The identified genes may serve as promising targets for genetic engineering to accelerate the breeding process for G. barbadense and the high-density genome variation map constructed in this work may facilitate our understanding of the genetic architecture of cotton traits.

Genetic basis of heterosis for yield and yield components explored by QTL mapping across four genetic populations in upland cotton.

BACKGROUND: Quantitative trait loci (QTL) mapping provides a powerful tool to unravel the genetic bases of cotton yield and its components, as well as their heterosis. In the present study, the genetic basis underlying inbreeding depression and heterosis for yield and yield components of upland cotton was investigated in recombinant inbred line (RIL), immortalized F2 (IF2), and two backcross (BCF1) populations based on a high-density SNP linkage map across four environments. RESULTS: Significant inbreeding depression of fruit branches per plant (FB), boll numbers per plant (BN), seed cotton yield (SY), and lint yield (LY) in RIL population and high levels of heterosis for SY, LY, and boll weight (BW) in IF2 and two BCF1 populations were observed. A total of 285 QTLs were identified in the four related populations using a composite interval mapping approach. In the IF2 population, 26.60% partially dominant (PD) QTLs and 71.28% over-dominant (OD) QTLs were identified. In two BCF1 populations, 42.41% additive QTLs, 4.19% PD QTLs, and 53.40% OD QTLs were detected. For multi-environment analysis, phenotypic variances (PV) explained by e-QTLs were higher than those by m-QTLs in each of the populations, and the average PV of m-QTLs and e-QTLs explained by QTL × environment interactions occupied a considerable proportion of total PV in all seven datasets. CONCLUSIONS: At the single-locus level, the genetic bases of heterosis varied in different populations. Partial dominance and over-dominance were the main cause of heterosis in the IF2 population, while additive effects and over-dominance were the main genetic bases of heterosis in two BCF1 populations. In addition, the various genetic components to heterosis presented trait specificity. In the multi-environment model analysis, epistasis was a common feature of most loci associated with inbreeding depression and heterosis. Furthermore, the environment was a critical factor in the expression of these m-QTLs and e-QTLs. Altogether, additive effects, over-dominance, epistasis and environmental interactions all contributed to the heterosis of yield and its components in upland cotton, with over-dominance and epistasis more important than the others.

QTL Mapping and Heterosis Analysis for Fiber Quality Traits Across Multiple Genetic Populations and Environments in Upland Cotton.

An "immortalized F2" (IF2) population and two reciprocal backcross (HSBCF1 and MARBCF1) populations were constructed to investigate the genetic bases of fiber quality traits in upland cotton across four different environments. A relatively high level of heterosis for micronaire (MIC) in IF2 population as well as fiber length (FL) and MIC in MARBCF1 population was observed. A total of 167 quantitative trait loci (QTLs) were detected in the three related experimental populations and their corresponding midparental heterosis (MPH) datasets using the composite interval mapping (CIM) approach. An analysis of genetic effects of QTLs detected in different populations and their MPH datasets showed 16 (24.24%) QTLs of partial dominance, and 46 (69.70%) QTLs of overdominance were identified in an IF2 population; 89 (62.68%) additive QTLs, three (2.11%) partial dominant QTLs, and 49 (34.51%) over-dominant QTLs were detected in two BCF1 populations. Multi-environment analysis showed 48 and 56 main-QTLs (m-QTLs) and 132 and 182 epistasis-QTLs (e-QTLs), by inclusive composite interval mapping (ICIM) in IF2 and two BCF1 populations, respectively. Phenotypic variance explained by e-QTLs, except for MARBCF1 population, was higher than that by m-QTLs. Thus, the overdominant, partial dominant, and epistasis effects were the main causes of heterosis in the IF2 population, whereas the additive, overdominant, and epistasis effects were the primary genetic basis of heterosis in the two BCF1 populations. Altogether, additive effect, partial dominance, overdominance, and epistasis contributed to fiber quality heterosis in upland cotton, but overdominance and epistasis were the most important factors.

New medium used in the differentiation of human pluripotent stem cells to retinal cells is comparable to fetal human eye tissue.

Human pluripotent stem cells (hPSCs) have the potential to differentiate along the retinal lineage. However, most induction systems are dependent on multiple small molecular compounds such as Dkk-1, Lefty-A, and retinoic acid. In the present study, we efficiently differentiated hPSCs into retinal cells using a retinal differentiation medium (RDM) without the use of small molecular compounds. This novel differentiation system recapitulates retinal morphogenesis in humans, i.e. hPSCs gradually differentiate into optic vesicle-shaped spheres, followed by optic cup-shaped spheres and, lastly, retinal progenitor cells. Furthermore, at different stages, hPSC-derived retinal cells mirror the transcription factor expression profiles seen in their counterparts during human embryogenesis. Most importantly, hinge epithelium was found between the hPSC-derived neural retina (NR) and retinal pigment epithelium (RPE). These data suggest that our culture system provides a new method for generating hPSC-derived retinal cells that, for the first time, might be used in human transplantation.

Heterogeneous nuclear ribonucleoprotein K, an RNA-binding protein, is required for optic axon regeneration in Xenopus laevis.

Axotomized optic axons of Xenopus laevis, in contrast to those of mammals, retain their ability to regenerate throughout life. To better understand the molecular basis for this successful regeneration, we focused on the role of an RNA-binding protein, heterogeneous nuclear ribonucleoprotein (hnRNP) K, because it is required for axonogenesis during development and because several of its RNA targets are under strong post-transcriptional control during regeneration. At 11 d after optic nerve crush, hnRNP K underwent significant translocation into the nucleus of retinal ganglion cells (RGCs), indicating that the protein became activated during regeneration. To suppress its expression, we intravitreously injected an antisense Vivo-Morpholino oligonucleotide targeting hnRNP K. In uninjured eyes, it efficiently knocked down hnRNP K expression in only the RGCs, without inducing either an axotomy response or axon degeneration. After optic nerve crush, staining for multiple markers of regenerating axons showed no regrowth of axons beyond the lesion site with hnRNP K knockdown. RGCs nonetheless responded to the injury by increasing expression of multiple growth-associated RNAs and experienced no additional neurodegeneration above that normally seen with optic nerve injury. At the molecular level, hnRNP K knockdown during regeneration inhibited protein, but not mRNA, expression of several known hnRNP K RNA targets (NF-M, GAP-43) by compromising their efficient nuclear transport and disrupting their loading onto polysomes for translation. Our study therefore provides evidence of a novel post-transcriptional regulatory pathway orchestrated by hnRNP K that is essential for successful CNS axon regeneration.