cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions.

Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants unanalyzed. In this work, we introduce cumulative LD (cLD), a stable statistic that captures the rare-variant LD between genetic regions, which reflects more biological interactions between variants, in addition to lack of recombination. We derived the theoretical variance of cLD using delta methods to demonstrate its higher stability than LD for rare variants. This property is also verified by bootstrapped simulations using real data. In application, we find cLD reveals an increased genetic association between genes in 3D chromatin interactions, a phenomenon recently reported negatively by calculating standard LD between common variants. Additionally, we show that cLD is higher between gene pairs reported in interaction databases, identifies unreported protein-protein interactions, and reveals interacting genes distinguishing case/control samples in association studies.

Identification of a recessive gene YrZ15-1370 conferring adult plant resistance to stripe rust in wheat-Triticum boeoticum introgression line.

KEY MESSAGE: A novel recessive gene YrZ15-1370 derived from Triticum boeoticum confers adult-plant resistance to wheat stripe rust. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most damaging diseases of wheat globally and resistance is the effectively control strategy. Triticum boeoticum Boiss (T. monococcum L. ssp. aegilopoides, 2n = 2x = 14, AbAb) accession G52 confers a high level of adult-plant resistance against a mixture of the Chinese prevalent Pst races. To transfer the resistance to common wheat, a cross was made between G52 and susceptible common wheat genotype Crocus. A highly resistant wheat-T. boeoticum introgression line Z15-1370 (F5 generation) with 42 chromosomes was selected cytologically and by testing with Pst races. F1, F2, and F2:3 generations of the cross between Z15-1370 and stripe rust susceptible common wheat Mingxian169 were developed. Genetic analysis revealed that the resistance in Z15-1370 was controlled by a single recessive gene, tentatively designated YrZ15-1370. Using the bulked segregant RNA-Seq (BSR-Seq) analysis, YrZ15-1370 was mapped to chromosome 6AL and flanked by markers KASP1370-3 and KASP-1370-5 within a 4.3 cM genetic interval corresponding to 1.8 Mb physical region in the Chinese Spring genome, in which a number of disease resistance-related genes were annotated. YrZ15-1370 differed from previously Yr genes identified on chromosome 6A based on its position and/or origin. The YrZ15-1370 would be a valuable resource for wheat resistance improvement and the flanking markers developed here could be useful tools for marker-assisted selection (MAS) in breeding and further cloning the gene.

Different frequency of acupoint thread-embedding for overweight/obesity of spleen deficiency and dampness retention: a randomized controlled trial. / ä¸åŒé¢‘æ¬¡ç©´ä½åŸ‹çº¿æ²»ç–—è„¾è™šæ¹¿é˜»åž‹è¶ é‡/è‚¥èƒ–ï¼šéšæœºå¯¹ç §è¯•éªŒ.

OBJECTIVES: To compare the effect of different frequency of acupoint thread-embedding on weight loss in subjects with overweight/obesity of spleen deficiency and dampness retention. METHODS: A total of 126 subjects with overweight/obesity of spleen deficiency and dampness retention were randomized into a 2-week group(63 cases, 13 cases dropped out)and a 3-week group(63 cases, 11 cases dropped out, 1 case was eliminated). The two groups were treated with acupoint thread-embedding once every 2 weeks and once every 3 weeks respectively, Zhongwan(CV 12), Shuifen(CV 9), Qihai(CV 6), Guanyuan(CV 4) and bilateral Zhangmen(LR 13), Tianshu(ST 25), Liangmen(ST 21), Daheng(SP 15), Fujie(SP 14), Pishu(BL 20), Yinlingquan(SP 9)were selected. Four times were required in the two groups. Before and after treatment, follow-up after 2 months of treatment completion, the body mass index(BMI), body weight, waist circumference, hip circumference, waist-to-hip ratio, obesity degree, fat percentage(F%), skin fold thickness were observed in the two groups. RESULTS: After treatment and in follow-up, the BMI, body weight, waist circumference, hip circumference, waist-to-hip ratio, obesity degree, F%, skin fold thickness in the two groups were decreased compared with those before treatment (P<0.001, P<0.01), the changes of BMI, body weight, obesity degree, F%, skin fold thickness in the 2-week group were larger than those in the 3-week group(P<0.05, P<0.01, P<0.001). CONCLUSIONS: The effect of acupoint thread-embedding once every 2 weeks on weight loss in subjects with overweight/obesity of spleen deficiency and dampness retention is superior to that once every 3 weeks.

Development and identification of four new synthetic hexaploid wheat lines with solid stems.

Stem solidness is an important agronomic trait for increasing the ability of wheat to resist lodging. In this study, four new synthetic hexaploid wheat with solid stems were developed from natural chromosome doubling of F1 hybrids between a solid-stemmed durum wheat (Triticum turgidum ssp. durum, 2n = 4x = 28, AABB) and four Aegilops tauschii (2n = 2x = 14, DD) accessions. The solid expression of the second internode at the base of the stem was stable for two synthetic hexalpoid wheat Syn-SAU-117 and Syn-SAU-119 grown in both the greenhouse and field. The lodging resistance of four synthetic solid-stem wheats is stronger than that of CS, and Syn-SAU-116 has the strongest lodging resistance, followed by Syn-SAU-119. The paraffin sections of the second internode showed that four synthetic wheat lines had large outer diameters, well-developed mechanical tissues, large number of vascular bundles, and similar anatomical characteristics with solid-stemmed durum wheat. The chromosomal composition of four synthetic hexaploid wheat was identified by FISH (fluorescence in situ hybridization) using Oligo-pSc119.2-1 and Oligo-pTa535-1. At adult stage, all four synthetic hexaploid wheat showed high resistance to mixed physiological races of stripe rust pathogen (CYR31, CYR32, CYR33, CYR34). These synthetic hexaploid wheat lines provide new materials for the improvement of common wheat.