Erythropoietin Receptor Gene （EPOR） Polymorphisms are Associated with Sow Litter Sizes

The erythropoietin receptor (EPOR) has shown to play an important role in fetal survival by promoting the maturation of red blood cells in many studies of uterine capacity and litter size in swine. In this study, we screened the porcine EPOR gene for mutations and identified five single nucleotide polymorphisms (SNPs): g.705G＞T in intron 1, g.2 373C＞T in intron 4, and g.2 882C＞T, g.3 035A＞G, and g.3 132A＞T in intron 6. We then genotyped 247 Beijing Black (BB) sows and compared the polymorphism data with the litter sizes of 1 375 parities among the sows. At first parity, there was no association of g.2 882C＞T and g.3 132A＞T with litter sizes. However, the CT sows in g.2 882C＞T had 2.13 higher total number born (TNB) (P＜0.01) and 1.81 higher number bom alive (NBA) (P＜0.01) than the CC sows and the heterozygous sows in g.3 132A＞Thad the highest litter size when compared to the two homozygotes for the later parities (P＜0.05). In the g.3 035A＞G SNP,for the later parities, the TNB of the sows with the GG genotype was 3.81 higher (P＜0.01) and the NBA was 2.75 higher(P＜0.01) than that with the AA genotype but no difference at first parity. The G allele of the EPOR g.705G＞T SNP wasassociated with a greater litter size at both the first parity (P＜0.05) and later parities (P＜0.01). Furthermore, we determined the allele frequencies for this SNP among five Chinese indigenous pig breeds (Erhualian, Laiwu Black, Meishan, Min, and Rongchang) and three western commercial pig breeds (Duroc, Landrace, and Large White). The G allele of the EPOR g.705G＞T SNP was significantly more common in the more prolific Chinese breeds. These results indicated that the EPOR could be an important candidate gene for litter size and g.705G＞T can serve as a useful genetic marker for improving litter size in both first and later parities in swine.     

鮸鱼EST-cSNP位点发掘及其特征分析

为发掘鮸鱼的EST-cSNP位点,以测序获得的鮸鱼脾脏4609条高质量表达序列标签(expressed sequence tags,EST)序列为源序列,利用Vector NTI 11.0软件拼接出707条重叠群(contig)序列,检测到209个可信度高的编码区单核苷酸多态性(coding-region single nucleotide polymorphism,cSNP)位点;SNP位点数在包含SNP序列中的发生概率为0.743%,在209个SNP位点中包含114个碱基转换位点、74个碱基颠换位点和21个插入缺失位点,转换与颠换比为1.54;对所鉴定的SNP位点的相关序列进行基因注释表明,这些序列包括一批与免疫抗逆相关的基因,例如主要组织相容性复合体、免疫球蛋白、T细胞受体以及各类蛋白酶等.说明所发掘的SNP将有助于促进鮸鱼的分子遗传学及分子辅助育种研究.     

小麦果聚糖合成酶基因6-SFT-A单核苷酸多态性分析及其定位

 【目的】小麦果聚糖合成酶基因6-SFT是果聚糖合成过程中的关键酶基因,研究6-SFT-A的多态性,分析其与小麦苗期抗旱性的关系,并进行遗传定位。【方法】以苗期抗旱性不同的30份六倍体小麦和4份小麦A基因组供体种乌拉尔图小麦为材料,通过直接测序分析6-SFT-A的单核苷酸多态性（SNP）及其与抗旱性的关系;开发基因分子标记,利用RIL群体（偃展1号×内乡188）对该基因进行遗传定位。【结果】在30份六倍体小麦材料中检测到14个核苷酸多态性位点,包括13个SNP和1个InDel,平均234 bp检测到一个多态性位点,仅在1 727和1 781 bp 2个位点检测到非同义突变;在4份乌拉尔图小麦中检测到28个SNP和4个InDel,其频率明显高于普通小麦。该基因的内含子1、2、3和外显子3为变异富集区,其它区域变异较小,外显子2变异最小,π值为0。34份材料分为3种单倍型,HaplⅠ主要包括中等抗旱材料和水敏感材料,Hapl Ⅲ中主要包括强抗旱材料和中等抗旱材料。利用RIL群体将该基因定位于染色体4A的标记Xcwm-27与Xwpt688之间,遗传距离分别为5.3和7.9 cM。【结论】单倍型分析表明,小麦果聚糖合成酶基因6-SFT-A单倍型与小麦苗期抗旱性有一定的相关性。     

基于高分辨率熔解曲线技术快速筛选黄瓜SNP1

为筛选用以黄瓜纯度检验和品种鉴定的SNP位点,以17个黄瓜杂交品种及其34份亲本为SNP筛选群体,利用高分辨率熔解曲线(high resolution melting,HRM)技术筛选SNP位点.本研究通过HRM分析和焦磷酸测序确认,获得CLA0(TT/--)、CLA1(C/T)和CLA6(A/G)三个SNP位点,群体...     

鹌鹑MC4R基因编码区群体遗传变异检测分析

 根据GenBank数据库提供的鹌鹑黑素促黑素受体4（MC4R）基因序列,设计出5对扩增引物,采用PCR SSCP分段检测方法对朝鲜鹌鹑MC4R基因外显子区域的多态性进行了检测,并对存在多态性的DNA片段进行了序列测定。SSCP分析的结果显示,第4号引物扩增的基因片段具有明显的多态性,并检测到了3种基因型（AA型,AB型,BB型）。将测序结果与GenBank数据库中鹌鹑MC4R基因序列进行比对,发现了一个单核苷酸多态性（SNP）位点：855bp位点存在一个T→C同义转换突变。基因型AA,AB和BB的频率分别为0.1933,0.6867和0.1200;等位基因A和B的频率分别为0.5367和0.4633;多态信息含量（PIC）和杂合度（H）分别为0.3736和0.4974;χ2检验的结果表明,该突变位点的基因频率未处于Hardy Weinberg平衡状态（P<0.01）。     

猪肉pHI和pHU相关SNP-QTL检测

以1个丹麦家猪家系为试验材料,对猪全基因组单核苷酸多态性(SNP)标记筛选与猪肉pHI和pHU值有关的QTL.结果发现在6号染色体上存在一个显著影响pHI和pHU值的QTL,与pHI显著相关的QTL的效应为2.6%~8.5%,其中单倍型FLJ30670的贡献率最高,为8.5%,与pHU显著相关的QTL中效应为2.1%~4.3%,都低于pHI有关的效应,其中效应最大的单倍型为FUT1,贡献率为4.3%,估计是猪肉24h酸度变化受外界其他因素的影响更多.     

牛LAP3基因内含子12和外显子13单核苷酸多态性

采用单链构象多态性(single-strand conformation polymorphism,SSCP)、创造酶切位点PCR(created restriction site-PCR, CRS-PCR)、限制性片段长度多态性(restriction fragment length polymorphism, RFLP)以及直接测序方法,研究中国荷斯坦牛、鲁西黄牛和渤海黑牛LAP3基因第12内含子和第13外显子的单核苷酸多态性(SNP)。共检测到5个SNP,分别为24 794（T/G）、24 803(T/C)、24 846（T/C）、24 564（G/A）和25 415（T/C）,其中24 564（G/A）为首次报道的位点。经PCR-SSCP结合测序图谱发现24 794（T/G）、24 803(T/C)、24 846（T/C）位点完全连锁,但该连锁位点在鲁西黄牛群体中未检测到。5个SNP位点在中国荷斯坦牛、鲁西黄牛和渤海黑牛群体的优势等位基因相同,分别是T、T、T、G、T,其等位基因频率分别是T（CH 0.579/LY 1/BB 0.722）、T（CH 0.579/LY 1/BB 0.722）、T（CH 0.579/LY 1/BB 0.722）、G(CH 0.584/ LY 0.775/BB 0.500)和T(CH 0.596/LY 0.796/BB 0.750),多态信息含量均在0.25至0.5之间,属于中度多态。     

稻米糊化温度的遗传与分子机理研究进展

糊化温度(gelatinization temperature, GT)是衡量稻米蒸煮品质和口感的重要参数之一。低GT稻米比高GT稻米蒸煮时需要较少的能量投入。支链淀粉的结构,特别是其分支链分布与GT密切相关,短链的含量越高,淀粉的GT越低。数量性状基因定位已经将GT相关基因定位在第6染色体的编码淀粉合酶IIa(SSⅡa)的alk基因位点。SSⅡa基因的若干功能性单核苷酸多态性(single nucleotide polymorphisms, SNPs)与GT和支链淀粉结构有关。这些SNPs已经用于标记辅助育种来改良稻米品质。提出了通过SSⅡa控制高或低GT的分子机理。     

Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.     

Characteristics of PCR fragments amplified using five microsatellite markers for identifying the Nagoya breed

The Nagoya breed is a native chicken of Aichi Prefecture, Japan, a dual‐purpose breed for eggs and meat. A method for distinguishing the Nagoya breed from Aichi Prefecture from other chickens using five microsatellite markers (ABR0015, ABR0257, ABR0417, ABR0495 and ADL0262) has already been utilized in order to check the authenticity of Nagoya breed‐labeled chicken on the market. The present study was conducted to investigate nucleotide sequences and sizes of PCR fragments containing the five microsatellite regions for the Nagoya breed and to confirm that the genomic identification could continue to be applied in the future. The DNA sequencing of fragments containing the five markers showed that ABR0015, ABR0417 and ABR0495 had a single haplotype, ABR0257 had three haplotypes, and ADL0262 had two haplotypes, although all the markers exhibited one fixed fragment size each upon sequencing of the fragments and fragment analysis. The results of the fragment analysis of each marker using DNA samples of 28 Nagoya breed males (G0 generation) reared in 2000–2001 and 20 of their offspring males (G8) reared in 2008–2009 showed one fixed fragment size in both populations. Therefore, we confirmed that the five microsatellite markers are useful tools for accurately distinguishing the Nagoya breed from other chickens.