Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

Key message

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton.

Abstract

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.

     

Sufficient-completeness, ground-reducibility and their complexity

Summary The sufficient-completeness property of equational algebraic specifications has been found useful in providing guidelines for designing abstract data type specifications as well as in proving inductive properties using the induction-less-induction method. The sufficient-completeness property is known to be undecidable in general. In an earlier paper, it was shown to be decidable for constructor-preserving, complete (canonical) term rewriting systems, even when there are relations among constructor symbols. In this paper, the complexity of the sufficient-completeness property is analyzed for different classes of term rewriting systems. A number of results about the complexity of the sufficient-completeness property for complete (canonical) term rewriting systems are proved: (i) The problem is co-NP-complete for term rewriting systems with free constructors (i.e., no relations among constructors are allowed), (ii) the problem remains co-NP-complete for term rewriting systems with unary and nullary constructors, even when there are relations among constructors, (iii) the problem is provably in almost exponential time for left-linear term rewriting systems with relations among constructors, and (iv) for left-linear complete constructor-preserving rewriting systems, the problem can be decided in steps exponential innlogn wheren is the size of the rewriting system. No better lower-bound for the complexity of the sufficient-completeness property for complete (canonical) term rewriting system with nonlinear left-hand sides is known. An algorithm for left-linear complete constructor-preserving rewriting systems is also discussed. Finally, the sufficient-completeness property is shown to be undecidable for non-linear complete term rewriting systems with associative functions. These complexity results also apply to the ground-reducibility property (also called inductive-reducibility) which is known to be directly related to the sufficient-completeness property.Some of the results in this paper were reported in a paper titled Complexity of Sufficient-Completeness presented at theSixth Conf. on Foundations of Software Technology and Theoretical Computer Science, New Delhi, India, Dec. 1986. The term quasi-reducibility is replaced in this paper by ground-reducibility as the latter seems to convey a lot more about the concept than the former.Partially supported by the National Science Foundation Grant nos. CCR-8408461 and CCR-8906678Partially supported by the National Science Foundation Grant nos. CCR-8408461 and CCR-9009414Partially supported by the National Science Foundation Grant no. DCR-8603184     

Antibodies to the Extracellular Pore Loop of TRPM8 Act as Antagonists of Channel Activation

The mammalian transient receptor potential melastatin channel 8 (TRPM8) is highly expressed in trigeminal and dorsal root ganglia. TRPM8 is activated by cold temperature or compounds that cause a cooling sensation, such as menthol or icilin. TRPM8 may play a role in cold hypersensitivity and hyperalgesia in various pain syndromes. Therefore, TRPM8 antagonists are pursued as therapeutics. In this study we explored the feasibility of blocking TRPM8 activation with antibodies. We report the functional characterization of a rabbit polyclonal antibody, ACC-049, directed against the third extracellular loop near the pore region of the human TRPM8 channel. ACC-049 acted as a full antagonist at recombinantly expressed human and rodent TRPM8 channels in cell based agonist-induced ⁴⁵Ca²⁺ uptake assays. Further, several poly-and monoclonal antibodies that recognize the same region also blocked icilin activation of not only recombinantly expressed TRPM8, but also endogenous TRPM8 expressed in rat dorsal root ganglion neurons revealing the feasibility of generating monoclonal antibody antagonists. We conclude that antagonist antibodies are valuable tools to investigate TRPM8 function and may ultimately pave the way for development of therapeutic antibodies.     

Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing

RAD sequencing was performed using DH962 and Jimian5 as upland cotton mapping parents. Sequencing data for DH962 and Jimian5 were assembled into the genome sequences of ≈55.27 and ≈57.06 Mb, respectively. Analysing genome sequences of the two parents, 1,323 SSR, 3,838 insertion/deletion (InDel), and 9,366 single-nucleotide polymorphism (SNP) primer pairs were developed. All of the SSRs, 121 InDels, 441 SNPs, and other 6,747 primer pairs were screened in the two parents, and a total of 535 new polymorphic loci were identified. A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population. Twenty-seven new QTLs for yield and fibre quality were identified, indicating that the efficiency of QTL detection was greatly improved by the increase in map density. Comparative genomics showed there to be considerable homology and collinearity between the A_T and A₂ genomes and between the D_T and D₅ genomes, although there were a few exchanges and introgressions among the chromosomes of the A₂ genome. Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed. This map can be used for molecular marker-assisted selection in cotton.     

KCNQ1 and type 2 diabetes: study in Hubei Han Chinese and meta-analysis in East Asian populations

Recent genome-wide association studies in East Asian poulations reported the association of KCNQ1 variants with type 2 diabetes. In the present study, we first investigated the association between rs2237892 in KCNQ1 and type 2 diabetes in a Hubei Han Chinese population (223 type 2 diabetes patients and 201 controls). The frequencies of CC genotype and C allele in type 2 diabetes patients were significantly higher than those of controls group (CC: 51.6% vs 39.3%, P=0.001; C: 72.2% vs 61.2%, P=0.001). The odds ratio for the risk allele C was 1.65 (95%CI 1.23–2.2, P=0.001). Then, we systematically reviewed the association of SNPs (rs2237892, rs2237895, rs2237897, rs2074196) in KCNQ1 with type 2 diabetes risk in a meta-analysis. Significant heterogeneity between studies was found for SNPs rs2237892 and rs2237897. Combined odds ratios of the rs2237892 C, rs2237895 C, rs2237897 C, rs2074196 G allele were 1.35 (95% CI 1.29–1.41, P<0.0001), 1.27 (95%CI 1.23–1.32, P<0.0001), 1.32 (95%CI 1.21–1.43, P<0.0001), 1.30 (95%CI 1.25–1.35, P<0.0001) respectively. Our results and meta-analysis demonstrated that KCNQ1 polymorphisms were reproducibly associated with the risk of type 2 diabetes in Han Chinese and East Asian populations.     

Metabolic profiling by ultra-performance liquid chromatography-mass spectrometry and parallel factor analysis for the determination of disease biomarkers in Eucalyptus

In this article, we present and discuss an alternative for data analysis of the metabolic profiles of both healthy Eucalyptus globulus and those infected with the Mycosphaerella leaf disease. The crude extracts were analyzed by reversed-phase ultra performance liquid chromatography-mass spectrometry. In order to glean the most useful information from these complex measurements, parallel factor analysis (PARAFAC) was employed for pattern recognition. After PARAFAC modeling, inspection of the scores and loadings graph allowed distinction of the healthy from the infected E. globulus samples and determination of biomarkers related to the biotic stress. The assessment of the monoisotopic masses and the fragmentation patterns allowed the identification of these biomarkers. It is hoped that the proposed method can be used for the diagnosis of diseases in plants, as well as to provide additional insight into the plant’s defense mechanism. Potentially, this may demonstrate the advantages of employing high order chemometric techniques in metabolomic data analysis.     

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.)

Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole‐genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome‐wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.     

miR169 and PmRGL2 synergistically regulate the NF-Y complex to activate dormancy release in Japanese apricot (Prunus mume Sieb. et Zucc.)

Plant Molecular Biology - This study is the first to demonstrate that GA4-induced dormancy release is associated with the NF-Y complex, which interacts with gibberellin inhibitor RGL2 in Japanese...