Detection of selection signatures of population‐specific genomic regions selected during domestication process in Jinhua pigs

Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome‐wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross‐population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population‐specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds.     

Whole-Genome Analysis Revealed the Positively Selected Genes during the Differentiation of indica and Temperate japonica Rice

To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93–11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I.     

A Method of Three-Dimensional Recording of Mandibular Movement Based on Two-Dimensional Image Feature Extraction

Background and Objective

To develop a real-time recording system based on computer binocular vision and two-dimensional image feature extraction to accurately record mandibular movement in three dimensions.

Methods

A computer-based binocular vision device with two digital cameras was used in conjunction with a fixed head retention bracket to track occlusal movement. Software was developed for extracting target spatial coordinates in real time based on two-dimensional image feature recognition. A plaster model of a subject’s upper and lower dentition were made using conventional methods. A mandibular occlusal splint was made on the plaster model, and then the occlusal surface was removed. Temporal denture base resin was used to make a 3-cm handle extending outside the mouth connecting the anterior labial surface of the occlusal splint with a detection target with intersecting lines designed for spatial coordinate extraction. The subject''s head was firmly fixed in place, and the occlusal splint was fully seated on the mandibular dentition. The subject was then asked to make various mouth movements while the mandibular movement target locus point set was recorded. Comparisons between the coordinate values and the actual values of the 30 intersections on the detection target were then analyzed using paired t-tests.

Results

The three-dimensional trajectory curve shapes of the mandibular movements were consistent with the respective subject movements. Mean XYZ coordinate values and paired t-test results were as follows: X axis: -0.0037 ± 0.02953, P = 0.502; Y axis: 0.0037 ± 0.05242, P = 0.704; and Z axis: 0.0007 ± 0.06040, P = 0.952. The t-test result showed that the coordinate values of the 30 cross points were considered statistically no significant. (P<0.05)

Conclusions

Use of a real-time recording system of three-dimensional mandibular movement based on computer binocular vision and two-dimensional image feature recognition technology produced a recording accuracy of approximately ± 0.1 mm, and is therefore suitable for clinical application. Certainly, further research is necessary to confirm the clinical applications of the method.     

小立碗藓扩展蛋白基因家族的鉴定与生物信息学分析

扩展蛋白(Expansins,EXP)是一类基因家族,几乎参与了植物发育的全过程,从种子萌发到果实成熟都有扩展蛋白的参与。该研究利用生物信息学的方法对小立碗藓(Physcomitrella patens) Expansin基因家族成员进行鉴定,分析了其基因结构、染色体定位以及系统发生关系。结果表明:小立碗藓基因组中含有Expansin A(EXPA) 32个、Expansin-like A(EXLA) 6个,并未发现Expansin-like B(EXLB)及Expansin B(EXPB)。扩展蛋白氨基酸序列长度在228～290 aa之间,编码蛋白质具有两个保守的结构域Pollen_allerg_1和DPBB_1。蛋白质亚细胞定位预测结果表明:运用CELLO在线工具预测发现小立碗藓中约4/5的EXP家族基因定位于细胞外;而Euk-mPLoc预测结果则显示小立碗藓EXP基因家族成员全定位于细胞外。基因结构分析表明,小立碗藓中约68%Expansin基因有含有1～3个内含子。以上结果可为深入研究小立碗藓扩展蛋白基因的分子进化与生物学功能奠定基础。     

ReCGiP,a database of reproduction candidate genes in pigs based on bibliomics

Background  

Reproduction in pigs is one of the most economically important traits. To improve the reproductive performances, numerous studies have focused on the identification of candidate genes. However, it is hard for one to read all literatures thoroughly to get information. So we have developed a database providing candidate genes for reproductive researches in pig by mining and processing existing biological literatures in human and pigs, named as ReCGiP.     

中国兽类名录(2021版)

中国是全球兽类物种多样性最高的国家之一,掌握我国兽类物种多样性和分类地位是兽类学研究的基础前提,也是科学保护野生种群的前提。为厘清中国兽类的物种数量及分类地位等关键分类学信息,中国动物学会兽类学分会组织国内长期致力于兽类各类群分类的科学研究人员,在总结前人研究的基础上,根据最新的形态学和分子遗传学证据,综合现代兽类分类学家意见,经编委会充分讨论,形成了最新的中国兽类名录,包括我国现阶段兽类12目59科254属686种。该中国兽类名录使用基于系统发生关系的分类系统,并对物种有效性进行了充分慎重的确认和讨论。     

EARLY SENESCENCE1 Encodes a SCAR-LIKE PROTEIN2 That Affects Water Loss in Rice

The global problem of drought threatens agricultural production and constrains the development of sustainable agricultural practices. In plants, excessive water loss causes drought stress and induces early senescence. In this study, we isolated a rice (Oryza sativa) mutant, designated as early senescence1 (es1), which exhibits early leaf senescence. The es1-1 leaves undergo water loss at the seedling stage (as reflected by whitening of the leaf margin and wilting) and display early senescence at the three-leaf stage. We used map-based cloning to identify ES1, which encodes a SCAR-LIKE PROTEIN2, a component of the suppressor of cAMP receptor/Wiskott-Aldrich syndrome protein family verprolin-homologous complex involved in actin polymerization and function. The es1-1 mutants exhibited significantly higher stomatal density. This resulted in excessive water loss and accelerated water flow in es1-1, also enhancing the water absorption capacity of the roots and the water transport capacity of the stems as well as promoting the in vivo enrichment of metal ions cotransported with water. The expression of ES1 is higher in the leaves and leaf sheaths than in other tissues, consistent with its role in controlling water loss from leaves. GREEN FLUORESCENT PROTEIN-ES1 fusion proteins were ubiquitously distributed in the cytoplasm of plant cells. Collectively, our data suggest that ES1 is important for regulating water loss in rice.Rice (Oryza sativa) is a major worldwide food crop, but it consumes more water than most crops (Linquist et al., 2015), with water consumption for rice cultivation accounting for approximately 65% of agricultural water usage. Rice provides a staple food for about 3 billion people while using an estimated 24% to 30% of the world’s developed freshwater resources (Bouman et al., 2007). Severe water shortages restrict the expansion of rice production and hinder the irrigation of existing paddy fields (Zhu and Xiong, 2013). One effective way to overcome water shortages is to reduce water loss in rice plants, thus allowing the cultivation of this key crop in environments with less water (Nguyen et al., 1997).In plants, the stomata on the leaf surface work as the main channels for the discharge of water and the entry of carbon dioxide, thus strongly affecting physiological processes such as transpiration and photosynthesis. Previous studies showed that mutations in some genes could affect stomatal density or differentiation, such as the Arabidopsis (Arabidopsis thaliana) genes TOO MANY MOUTHS (AtTMM; Yang and Sack, 1995), SCREAM2 (SCRM2; Kanaoka et al., 2008), STOMATA DENSITY AND DISTRIBUTION1 (AtSDD1; Von Groll et al., 2002), and AtYODA2, a mitogen-activated protein kinase kinase kinase (Bergmann et al., 2004). Stomata show a regular distribution on rice leaves (Huang et al., 2009) during plant growth and development, and various environmental factors affect the density and size of stomata as well as the chlorophyll contents of rice leaves. For example, rice leaves that develop under water stress show substantially fewer stomata compared with leaves that develop under well-watered conditions (Huang et al., 2009). Changes in stomatal density and morphology affect water loss (Boonrueng et al., 2013). In rice, SIMILAR TO RADICAL-INDUCED CELL DEATH1 enhances drought tolerance by regulating stomatal closure (You et al., 2013), while the zinc finger protein DROUGHT AND SALT TOLERANCE functions in drought and salt tolerance by adjusting stomatal aperture (Huang et al., 2009). In Arabidopsis, overexpression of the magnesium chelatase H subunit in guard cells confers drought tolerance by promoting stomatal closure (Tsuzuki et al., 2013). Thus, stomatal closure and low stomatal density enhance drought tolerance by reducing water loss in plants.The epicuticular wax layer in plants acts as the first barrier to environmental conditions by reducing water loss due to transpiration and preventing plant damage due to excessively strong sunlight (Riederer and Schreiber, 2001). Leaf transpiration involves both stomatal and cuticular transpiration. Stomatal conductance controls stomatal transpiration, but the physicochemical properties of the leaf surface mainly control cuticular transpiration. For example, the composition, thickness, and microstructure of the cuticular wax affect water permeability and transport (Svenningsson, 1988; Xu et al., 1995; Buschhaus and Jetter, 2012). Rice DROUGHT-INDUCED WAX ACCUMULATION1, GLOSSY1, and WAX SYNTHESIS REGULATORY GENE1 affect drought tolerance by regulating the deposition or biosynthesis of cuticular wax (Islam et al., 2009; Wang et al., 2012; Zhou et al., 2013; Zhu and Xiong, 2013).Besides, leaf trichomes can also affect water loss (Konrad et al., 2015) and leaf trichomes closely linked with the actin cytoskeleton. The involvement of the actin cytoskeleton in controlling directional cell expansion in trichomes has received much attention (Zhang et al., 2005). Generally, genes that affect cytoplasmic organization can be studied by screening leaf trichome mutants (Qiu et al., 2002). In Arabidopsis, a reproducible morphogenetic program directs the polarized development of trichome branches (Mathur et al., 1999; Szymanski et al., 1999; Le et al., 2006). Some of these genes affect the cytoskeleton and also affect the morphology of normal plant cells, especially epidermal cells. For example, mutation of SPIKE1 in Arabidopsis causes epidermal cells to show simple arrangements and morphologies (i.e. all cells dividing along a single axis; Qiu et al., 2002).To study the molecular mechanisms underlying water loss in rice, we isolated and characterized the early senescence1-1 (es1-1) rice mutant, which showed excessive water loss and early senescence phenotypes. Map-based cloning data showed that ES1 encodes a SCAR-LIKE PROTEIN2, and its Arabidopsis homolog affects the polymerization of actin. The es1-1 mutants showed obvious changes in leaf trichomes, similar to Arabidopsis. However, few studies have reported a connection between the actin cytoskeleton and water loss in Arabidopsis. Our results demonstrated a critical role of the actin cytoskeleton in regulating water loss in rice.