GDFs基因家族候选基因对崇仁麻鸡生长性状的影响

利用崇仁麻鸡差异性状的重测序结果,将生长分化因子(GDFs)基因家族作为候选基因,筛选与崇仁麻鸡生长性状相关的多态位点。结果发现,GDF-2、GDF-8和GDF-10基因的多态位点对崇仁麻鸡的生长性状有着显著或极显著的影响。单倍型分析结果显示,GDF-2和GDF-10基因的单倍型H3H3为劣势单倍型组合可以选择淘汰。研究结果表明,GDFs基因家族候选基因对崇仁麻鸡的生长性状有一定的影响。     

Quantitative trait loci for fruit size and flowering time-related traits under domestication and diversifying selection in cucumber (Cucumis sativus)

In cucumber, the genetic basis of traits under domestication and/or diversifying selection is not well understood. Here, we reported QTL mapping for flowering time and fruit size-related traits with segregating populations derived from a cultivated × wild cross. Phenotypic data of flowering time (FT), fruit size (FS), fruit number (FN) and fruit weight per plant (FW) were collected in multiple environments. QTL analysis identified 19 QTL for these traits. We found that the major-effect QTL FT1.1 played an important role in regulating flowering time in cultivated cucumber, whereas the minor-effect QTL FT6.3 contributed to photoperiod sensitive flowering time during domestication. Two novel consensus FS QTL, FS1.4 and FS2.3, seem to be the targets of selection during breeding for the US processing cucumber. All other FS QTL were co-localized with previously detected QTL using populations derived from cultivated cucumbers, suggesting that they were under selection during both initial domestication and subsequent improvement. Results from this study also suggested that the wild cucumber is a useful resource for capturing positive transgressive segregation and novel alleles that could be explored in cucumber breeding.     

An efficient method to produce segregating populations in quinoa (Chenopodium quinoa)

Quinoa offers a promising alternative for staple food, considering its outstanding nutritional value and tolerance to abiotic stresses. To develop breeding programmes in quinoa, a reliable crossing method for increasing the genetic variation is required. In the following study, we aimed to develop segregating populations in quinoa. We tested the efficiency of three different crossing methods (hand emasculation, warm water emasculation and no emasculation). Moreover we developed a two-stage selection strategy based on morphological traits and molecular markers for the selection of hybrid plants. We reported hand emasculation to be the most efficient crossing method, followed by warm water emasculation and no emasculation. Our results demonstrated that crosses in quinoa can be successfully performed, despite its complicated flower structure and high self-pollination rate. Additionally, we developed 30 segregating populations from crosses between accessions of different origins with varying phylogenetic relationship, which offers a promising perspective for quinoa breeding programmes in the future.     

鸡无尾性状的分子机制研究进展

动物的尾巴具有改变方向、控制升降、调整速度、支撑身体、防御、攻击、保温、示警、逃生和捕食等作用。鸟类的尾巴在飞行过程中起到平衡身体的关键作用，但在进化过程中尾部却出现了缩短和融合现象，如中国的瓢鸡及智利的Araucana鸡。作者简述了近年来关于鸡无尾性状的解剖学研究成果，发现无尾鸡在胚胎发育HH19期（Hamburger和Humilton标准分期）就已经出现无尾现象，而在结构上无尾鸡缺乏尾脂腺、尾羽、镰羽、尾椎骨和尾综骨。同时作者分析了导致尾部体节停止发育的分子遗传机制，包括周期性表达基因的转录调控影响尾部延伸过程、后端化因子梯度诱导尾部形成、Hox基因影响体节特化过程及基因突变有可能导致的无尾现象等，从而提出了可能导致家禽无尾性状的胚胎发育时期的关键分子及信号通路，包括Irx1和Irx2基因、Notch信号通路、Wnt信号通路、Fgf信号通路、RA信号通路等。研究鸡无尾性状的分子机制不仅可深入了解脊椎动物胚胎发育中尾部发育机制，更有利于揭示鸟类在进化过程中发生的尾部缩短及融合的机理。     

基于S基因序列分析新型猪流行性腹泻病毒的遗传演化

最近，笔者实验室在青藏高原地区发现两种新亚型藏猪源猪流行性腹泻病毒（PEDV），为进一步调查新型PEDV是否在四川腹泻猪群中存在或流行，对实验室2018-2019年保存的116份猪腹泻粪便或肠组织样本进行PEDV的检测及其纤突蛋白基因（spike）分子特征研究。结果表明：腹泻样本的PEDV检出率为42.2%（49/116，95% CI=33.1%~51.8%），并获得了13条完整的S基因序列，全长为4 149~4 170 bp，序列相似性为94.2%~99.9%，其中SWUN-H3-CH-SCYA-2019的S基因与藏猪源新G1亚群PEDV的序列相似性高达97.0%~98.6%。遗传演化研究结果表明13株PEDV S基因划分为G1和G2大群，其中SWUN-H3-CH-SCYA-2019位于藏猪源新G1亚群；SWUN-19-CH-SCZY-2018、SWUN-4-CH-SCXC-2018、SWUN-1-CH-SCNJ-2019和SWUN-3CH-CH-SCZG-2019位于G2亚群中一个独立的分支，且与藏猪源新G2亚群毒株有着较近的亲缘关系。为了进一步研究13株PEDV的演化过程，以贝叶斯进化分析软件包（BEAST）进行分歧时间估算，结果表明SWUN-H3-CH-SCYA-2019的分歧时间约为2012.3年，早于藏猪源新G1亚群其余毒株的最早分歧时间（2015.7年）；SWUN-4-CH-SCXC-2018、SWUN-19-CH-SCZY-2018和SWUN-3CH-CH-SCZG-2019的分歧时间约为2014.2年，早于G2亚群的藏猪源毒株2014.7年，所有藏猪源PEDV的分歧时间均晚于四川毒株。本研究在四川地区首次发现了藏猪源PEDV，并且从毒株的分歧时间推断青藏高原的藏猪源PEDV来源于四川，为新型PEDV分子遗传进化的监测提供了依据。     

Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.     

基于改进极限学习机的水体溶解氧预测方法

为了有效地指导水产养殖生产，提高溶解氧浓度预测的精度，提出了基于因子筛选和改进极限学习机（Extreme Learning Machine，ELM）的水产养殖溶解氧预测模型。首先，利用皮尔森相关系数法计算各影响因子与溶解氧浓度间的相关系数，提取强关联因子，降低预测模型的输入量维度；采用偏最小二乘算法（Partial Least Square, PLS）优化传统ELM神经网络，避免网络中隐含层共线性问题，保障输出权值的稳定性；然后，结合新型激活函数，构建水体溶解氧浓度预测模型。最后，将SPLS-ELM（Selection Based Partial Least Square Optimized Extreme Learning Machine）预测模型应用到江苏省无锡市南泉基地某试验池塘的水体溶解氧预测中。试验结果表明：该模型的预测均方根误差为0.3232，与最小二乘支持向量机（Least Square Support Vector Machine，LSSVM）、BP神经网络、粒子群（Particle Swarm Optimization，PSO）优化LSSVM和遗传算法（Genetic Algorithm, GA）优化BP神经网络相比分别降低40.98%、44.48%、34.73%和44.18%。且该模型的运行时间仅0.6231s，预测精度和运行效率明显优于其他模型。该模型的溶解氧预测曲线接近真实溶解氧变化曲线，能够满足水产养殖实际生产对水体溶解氧预测的要求。     

粳稻柱头外露率QTL定位

【目的】柱头外露是影响杂交水稻制种的一个重要性状。本研究旨在初步鉴定控制柱头外露率的QTL。【方法】以高柱头外露率粳稻两系不育系大S×低柱头外露率热带粳稻品系D50的F_2群体及海南陵水、浙江杭州两地重复种植的F_(2:3)群体为材料,考查F_2群体及陵水、杭州两地两次重复F_(2:3)群体单边柱头外露率(PSES)、双边柱头外露率(PDES)和柱头总外露率(PES)。【结果】相关分析表明,单边柱头外露率、双边柱头外露率和柱头总外露率之间存在极显著的正相关。根据构建的大S×D50 F_2群体遗传连锁图谱,QTL分析检测到水稻柱头外露率QTL 21个,分布于第1、2、3、4、6、7和12染色体上,贡献率变幅为0.1%~57.6%,除个别贡献率极低的位点外,绝大部分QTL加性效应来自于高值亲本大S。其中位于第4染色体和第12染色体的两个位点q PDES4,q PES12在F_2和两次重复F_(2:3)群体中均检测到,贡献率分别达17.86%和16.98%。位于第3染色体的q PES3位点在陵水、杭州两次F_(2:3)群体中重复检测到,贡献率高达25.6%。【结论】检测到的QTL,有些与其他学者报道的处于同一位置,有些则是新的柱头外露率QTL。这些水稻柱头外露率QTL为今后柱头外露率基因精细定位、克隆、以及利用分子标记辅助选择(MAS)选育高柱头外露率粳型不育系提供理论依据。     

Analysis of residuals for stability assessment of rice genotypes

The analysis of residuals computes general adaptabilities (GAs) and specific adaptabilities (SAs) of genotypes similar to combining ability analysis. The residual analysis is simple and robust being based on the first-degree statistics, and is assumption-free. A unique statistic of ratio of variances (VR) of residuals for individual genotypes allows comparing their stability. The residuals analysis of genotype × environment (GE) interactions was performed for grain yield (t ha^?1) of 25 rice (Oryza sativa L.) genotypes, including two developed by marker-assisted selection for root traits quantitative trait loci (QTL), tested across 16 sites. Results were compared with the linear regression analysis for (i) full set of 16 sites showing adequacy of linear model and (ii) subset of nine-poor sites showing inadequacy of linear model. There was agreement between the two analyses for situation (i) but not for situation (ii) when the regression analysis fails because of nonlinearity but the residual analysis retains its validity.     

鹰嘴豆短肽的分步酶解法制备及其营养价值评价

以鹰嘴豆蛋白为原料,建立复合酶分步酶解法制备鹰嘴豆短肽的工艺。在鹰嘴豆蛋白碱性蛋白酶Alcalase水解的基础上,进一步采用中性蛋白酶和风味蛋白酶Flavourzyme继续水解鹰嘴豆蛋白碱性蛋白酶Alcalase酶解物,并对各影响因素进行研究,建立短肽得率与各影响因素的回归模型,利用高效液相色谱法和氨基酸自动分析仪等测定鹰嘴豆短肽的相对分子质量、氨基酸组成、一般营养成分,评价鹰嘴豆短肽的营养价值。结果表明,中性蛋白酶和风味蛋白酶Flavourzyme制备鹰嘴豆短肽的最佳工艺参数为:复合酶添加量5 678 U/g,pH 7.0,水解时间216 min,水解温度55℃,在此条件下,短肽得率为63.79%,与碱性蛋白酶Alcalase单独酶解相比明显提高,水解度为26.74%;大部分水解产物的相对分子质量低于1 000、脂肪含量低,蛋白质、必需氨基酸等含量丰富,与FAO/WHO推荐的成人需求量模式相比,其第一限制氨基酸是蛋氨酸和半胱氨酸,与学龄儿童需求量模式相比,其第一限制氨基酸是苏氨酸,氨基酸分分别高达138.18和103.25;必需氨基酸与非必需氨基酸比值(EAA/NEAA)为0.73,接近FAO/WHO参考标准值0.6。该研究为进一步开发利用和工业化生产鹰嘴豆短肽奠定了基础。