Associations of Gonadotropin-Releasing Hormone Receptor (GnRHR) and Neuropeptide Y (NPY) Genes'''' Polymorphisms with Egg-Laying Traits in Wenchang Chicken

Single nucleotide polymorphisms (SNP) of chicken gonadotropin-releasing hormone receptor (GnRHR) and neuropeptide Y (NPY) were selected to identify the genotypes of Wenchang (Chinese indigenous breed) chicken with restricton fragment length polymorphisms. The associations of the SNPs with the total egg production (NE), average days of continual laying (ADCL), and number of double-yolked eggs (DYE) traits were analyzed. The frequency of restriction enzyme A/a alleles in the population was for GnRHR 0.69 (Bpu1102 Ⅰ A) and 0.31 (Bpu1102 Ⅰ a) and for NPY 0.46 (Dra Ⅰ B) and 0.54 (Dra Ⅰ b). Trait data from a total of 120 hens, which were purebred introduced from Hainan Province, China from one generation were recorded. Two significant effects of genes' marker were found for GnRHR and number of eggs (dominant; t= 2.67, df= 116) and NPY and number of eggs (additive; t= 1.97, df= 116). The current research supports the effects of GnRHR and NPY genes on egg-laying traits of chickens.     

Construction of Genetic Linkage Map Based on SSR Markers in Peanut （Arachis hypogaea L.）

Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci （QTLs） for morphological, physiological and economic traits of crop species. However, a comprehensive genetic linkage map for cultivated peanut has not yet been developed due to the extremely low frequency of DNA polymorphism in cultivated peanut. In this study, 142 recombinant inbred lines （RILs） derived from a cross between Yueyou 13 and Zhenzhuhei were used as mapping population in peanut （Arachis hypogaea L.）. A total 652 pairs of genomic-SSR primer and 392 pairs of EST-SSR primer were used to detect the polymorphisms between the two parents. 141 SSR primer pairs, 127 genomic-SSR and 14 EST-SSR ones, which can be used to detect polymorphisms between the two parents, were selected to analyze the RILs population. Thus, a linkage genetic map which consists of 131 SSR loci in 20 linkage groups, with a coverage of 679 cM and an average of 6.12 cM of inter-maker distance was constructed. The putative functions of 12 EST-SSR markers located on the map were analyzed. Eleven showed homology to gene sequences deposited in GenBank. This is the first report of construction of a comprehensive genetic map with SSR markers in peanut （Arachis hypogaea L.）. The map presented here will provide a genetic framework for mapping the qualitative and quantitative trait in peanut.     

Correlation Analysis on Single Nucleotide Polymorphism of CAPN1 Gene and Meat Quality and Carcass Traits in Chickens

The selection of meat quality has received considerable focus in chicken breeding. This study was aimed at investigating the effect of CAPN1 gene on meat quality traits in chicken populations. Primer pairs for 3 UTR in CAPN1 were designed from database of chicken genomic sequence. Polymorphisms were detected using PCR-SSCP and DNA sequencing. A mutation at position 9 950 nt （G/A, locus A） was found among individuals in each population. The allele and genotype frequencies significantly differed among eight lines with higher frequencies of allele A2 and genotype AIA2 （P〈0.01）. The least square analysis showed that there was significant difference （P 〈 0.05） in muscle fiber density and some carcass traits among genotypes and that the breast muscle fiber density （BFD） of birds ofAIA1 genotype was significantly higher （P〈0.05） than that of birds ofA2A2 genotype. It was concluded that the CAPN1 gene was the major gene affecting the muscle fiber traits of chicken or was linked with the major gene. These results were useful for studying the molecular mechanism that influences meat traits and were used as the base of molecular-assisted selection to meat quality traits. So, this site may be a potential marker affecting the muscle traits of chickens.     

Major Gene Identification and Quantitative Trait Locus Mapping for Yield- Related Traits in Upland Cotton （Gossypium hirsutum L.）

Segregation analysis of the mixed genetic model of major gene plus polygene was used to identify the major genes for cotton yield-related traits using six generations P1, P2, F1, B1, B2, and F2 generated from the cross of Baimian 1 x TM-1. In addition to boll size and seed index, the major genes for the other five traits were detected： one each for seed yield, lint percentage, boll number, lint index; and two for lint yield. Quantitative trait locus/loci （QTL） mapping was performed in the F2 and F2：3 populations of above cross through molecular marker technology, and a total of 50 QTL （26 suggestive and 24 significant） for yield-related traits were detected. Four common QTL were discovered： qLP-3b（F2）/qLP-3（F2：3） and qLP-19b （F2）/qLP-19（F2：3） for lint percentage, qBN-17（F2）/qBN-17（F2：3） for boll number, and qBS-26b（F2）/qBS-26（F2：3） for boll size. Especially, qLP- 3b（Fz）/qLP-3（F2：3）, not only had LOD scores 〉3 but also exceeded the permutation threshold （5.13 and 5.29, respectively）, correspondingly explaining 23.47 and 29.55% of phenotypic variation. This QTL should be considered preferentially in marker assisted selection （MAS）. Segregation analysis and QTL mapping could mutually complement and verify, which provides a theoretical basis for genetic improvement of cotton yield-related traits by using major genes （QTL）.     

Variations of Single Nucleotide Polymorphism （SNP） of Hordoindoline a Gene （hina） and Its Relationships with Kernel Hardness in 92 North American Barley Varieties （Hordeum vulgare L.）

Grain texture in barley （Hordeum vulgare L.） is an important quality character. The single nucleotide polymorphisms （SNPs） in Hordoindoline a （hina） gene and its relationship with hardness index among North American harley cultivars were investigated. The hina genes in 36 cultivars were sequenced for the SNP analyses, and 17 sets of SNP primers were designed to detect the SNP variations of hina locus in 92 North American barley cultivars. SNP detection indicated that there were four haplotypes in the hina genes of 92 barley cultivars, and haplotype 01 and 02 were shared by 68 and 14 cultivars, respectively, suggesting that there was a very limited diversity in hina genes among North American barley cultivars. Despite the wide range in hardness exists in 92 barley cultivars, however, unlike wheat, where a clear relationship has been demonstrated between a number of SNPs in the wheat hardness genes and quality （soft or hard wheat）, there was no such relationship for barley. The genotypes used in this study demonstrated that there was a low level of polymorphism in hina gene in North American barley cultivars and these polymorphisms had no impact on grain hardness.     

Polymorphism analysis of microsatellites and construction of linkage map in part regions of four chromosomes in chicken

Based on chicken' consensus map issued in 2000,17 microsatellites near 4 candidate genes such as IGF2,OBR,GDF8 and APOA1 in 4 chromosomes(chromosome 5,7,8 and 24)were chosen for polymorphism analysis and construction of linkage map.Combining the technique of PCR and the fluorescent semi-automated detection,genome scanning was performed for 440 chickens,which was derived from China Agricultural University chicken resource families within three generations.The individuals of this resource families were genotyped.The results showed that the number of alleles ranged from 4 to 14;heterozygosity(H) of markers was between 0.3116 and 0.9148.Polymorphic information content(PIC)varied from 0.2672 to 0.8679.Microsatellites along with above-mentioned 4 candidate genes doing as general markers were used to construct linkage map.The spans of 4 linkage maps constructed in the part region of chromosome 5,7,8 and 24 were 263.5,79.9,206.2 and 104.2 cM,respectively.The order of markers was consistent with that of counterpart of reported consensus map.However,The spans of linkage map were larger than that of consensus map.The constructed linkage maps laid the foundation for mapping quantitative trait loci(QTL)responsible for economically important traits in chicken.     

Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

Birth weight(BW) and days to 100 kg(D100) are important economic traits that are both affected by polygenes. However, the genetic architecture of these quantitative traits is still elusive. Genotyping-by-sequencing(GBS) data containing a large number of single nucleotide polymorphisms(SNPs) have become a powerful tool in genomic analysis. To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology. After quality control, 279 787 SNPs were generated for subsequent genome-wide association study(GWAS). A total of 30 genome-wide SNPs(P1.79 E–07) were identified for D100. Furthermore, a total of 22 and 2 suggestive SNPs(P3.57 E–06) were detected for D100 and BW, respectively. Of these, one locus located on SSC12(position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits. Considering the function of candidate genes, two genes, NSRP1 and DOCK7, were suggested as the most promising candidate genes involved in growth traits. Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.     

Multiple Interval Mapping for Whole Cocoon Weight and Related Economically Important Traits QTL in Silkworm （Bombyx mort）

A backcrossed population （BC1） derived from a cross between C100 and Dazao was obtained. The quantitative trait loci （QTLs） of the economically important traits for whole cocoon weight, cocoon shell weight, ratio of cocoon shell and weight of pupae, etc., were analyzed for the first time using the multiple interval mapping software WinQTLCart2.0. In total 40 QTLs were detected and contributed to 21 groups based on the constructed linkage map. According to the mapping results, 2, 2, 3, and 2 major QTLs explained over 20% of total phenotypic variations, whereas four QTLs, namely qCW-19, qSW-2, qCSR-4, and qPW-23, explained more than 30% of total phenotypic variations for whole cocoon weight, cocoon shell weight, ratio of cocoon shell and weight of pupae, respectively. Correlated traits QTLs often share the same location. Furthermore, most of the detected QTLs were closed to one-side marker. By using the very closed markers, positive QTLs can be aggregated, which can form a basis for molecular marker-assisted selection and breeding.     

Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

Although quantitative trait loci(QTLs) for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes(SSCs) 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms(SNPs) associated with total number of thoracic-lumbar vertebrae and for each trait(number of thoracic and lumbar vertebrae) separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60 K chip. Performing a genome-wide association study(GWAS) for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor(NR6A1) on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin(VRTN), prospero homeobox 2(PROX2), Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog(FOS), and transforming growth factor beta 3(TGFB3) may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.     

Identification of Molecular Markers Linked to the Wilt Resistance Gene FuJ7（t） in Flax

A cross between wilt resistant flax variety Jinya7 and susceptible variety Jinyal was made for mapping wilt resistance gene(s). The inoculation test of F1 and F2 progeny proved that the resistance of Jinya7 to wilt is controlled by two dominant genes. With 48 EcoRⅠ /MseⅠ primer combinations, amplified fragment length polymorphisms (AFLP) analysis was performed on two parents and their F2 resistance and susceptibility bulks. A total of about 3 300 distinguishable bands were amplified, of which three bands had stable differences. The genetic linkage analysis of the three polymorphic DNA fragments with the resistance gene(s) was made in the F2 segregating population derived from the cross between Jinya7 and Jinyal. The DNA fragment AG/CAG was found closely linked to one of the wilt-resistant genes, which with a genetic distance of 5.2cm, was tentatively named FuJ7(t). The cloned fragment AG/CAG was sequenced and then converted successfully to a sequence characterized amplified region (SCAR) marker, which can be used more conveniently in the identification and marker-assisted selection for the wilt resistance gene FuJ7(t) to flax wilt.     

下丘脑-垂体-性腺轴上基因多态性与鸡冠高和体重的相关性分析

鸡冠高及体重是优质鸡早熟性选育过程中重要的参考指标,通过研究鸡多个侯选基因上突变位点与冠高和体重的相关性,寻找可作为该性状标记辅助选择的重要标记。在GnRH-I、GnRHR、NPY、DRD2、VIP、VIPR-1和PRL这7个侯选基因上共选取了10个多态位点,采用PCR-RFLP方法对1 310只宁都三黄鸡进行了基因型检测,并对各位点与77、84、91日龄冠高和体重性状的相关性进行了分析。结果表明:NPY基因上的2个位点I31391359D及C31394761T可作为91日龄体重标记辅助选择的有效分子标记;VIPR-1基因上的位点A1661691G可作为77、84日龄冠高的有效分子标记。     

神经肽(NPY)基因多态性与邵伯鸡母系繁殖性状的关联性分析

以神经肽(NPY)基因为候选基因,利用PCR-SSCP技术检测该基因的SNPs,并分析基因多态性与邵伯鸡母系母鸡的开产日龄、开产蛋重、开产体重以及300日龄总产蛋数之间的关联性。结果显示,在NPY基因上发现1个SNP位点,带有1对等位基因A和B,基因频率分别为0.35和0.65;不同基因型仅与开产体重性状间有显著相关,表现为基因型AA个体的平均开产体重比基因型AB个体的平均开产体重重119.03 g,且差异显著(P<0.05),基因型AA个体的平均开产体重比基因型BB个体的平均开产体重重47.6 g,但差异不显著(P>0.05);基因型BB个体的平均开产体重比基因型AB个体的平均开产体重重71.43 g,差异显著(P<0.05)。     

藏猪生长激素（pGH）基因多态性研究

猪生长激素（pGH）是猪生长发育性状重要的候选基因之一。采用PCR RFLP技术检测藏猪pGH基因+159～+734 bp片段的Dra I、Apa I和Msp I酶切多态性。结果显示,藏猪群体中Dra I酶切全部切开,无多态;Apa I酶切具有4个等位基因,出现5种基因型,其中CC基因型（299A/432C）频率最高,为0.7857;藏猪群体Msp I酶切出现3种基因型,杂合性CT基因型频率最高,为0.5089,等位基因C和T频率分别为0.5580和0.4420。经比较,藏猪pGH基因Dra I酶切位点与其他猪种一样无多态性,而Apa I酶切出现了特异的432突变位点,Msp I酶切等位基因分布相对均衡,表现出与其他猪种的差异。     

核受体辅激活蛋白1基因(NCOA1)作为鸡产蛋性状候选基因的研究

以清远麻鸡、白耳鸡、鹿苑鸡、藏鸡和S2系为试验素材,利用PCR-SSCP技术对核受体辅激活蛋白1(NCAO1)基因编码区进行SNP检测和基因型的判别,探讨NCAO1基因作为影响鸡产蛋性状候选基因的可能性。结果显示:在NCOA1基因的第3和第12外显子上分别发现一个SNP位点,其中第3外显子10155007处发生了T→A突变,检测到AA、AB、BB3种基因型;第12外显子108273423处发生了C→T突变,检测到CC、CD、DD3种基因型。χ2检验表明突变产生的基因型和基因频率在各品种(系)间差异极显著(P<0.01),A、C基因在蛋用型的地方品种白耳鸡中频率较高,B、D基因在肉用型的地方品种清远麻鸡、藏鸡和肉用型培育品系S2系鸡中频率较高。不同基因型与S2系鸡的开产日龄(AFE)、开产蛋重(WFE)、连产天数(CL)及300日龄产蛋数(EN)之间的最小二乘均数分析显示:AA基因型个体的连产天数比BB型个体多0.59 d,开产蛋重重0.6 g,300日龄产蛋量高7.76%,且差异显著(P<0.05);CC基因型个体比DD型个体的连产天数多0.51 d,开产蛋重重1.04 g,300日龄产蛋量高9.07%,且差异显著(P<0.05);组合基因型发现,基因型AACC个体的开产日龄、连产天数和300日龄产蛋量均高于BB、DD基因型组合。因而,初步推断NCOA1基因是影响鸡产蛋性状的主效基因或与主效基因连锁。     

促性腺激素释放激素受体基因(GnRHR)多态性及其与西农萨能奶山羊产羔性状关系的研究

在所选具有头3胎产羔记录的西农萨能奶山羊和布尔山羊群中检测促性腺激素释放激素受体基因(GnRHR)的多态性,根据检测结果分析GnRHR基因对产羔性状的影响。设计7对引物,采用单链构象多态(PCR-SSCP)技术检测该基因第1和第2外显子在西农萨能奶山羊和布尔山羊中的单核苷酸多态性。结果发现:引物P3和P7扩增片段具有多态性。P3扩增片段,在西农萨能奶山羊和布尔山羊都检测到AA和AB基因型,AB型与AA型相比在外显子1有+714缺失A和+731插入G二个突变;P7扩增片段,在布尔山羊中检测到CC和CD基因型,在西农萨能奶山羊中只检测到CC基因型,CD型与CC型相比在外显子2有+1440C→A一个突变。经过统计分析发现,西农萨能奶山羊AA和AB基因型频率分别为0.86和0.14,杂合体AB型平均产羔数比纯合体AA型多0.31只(P<0.05)。推测,GnRHR基因可能是控制山羊繁殖力的主效基因或是与之紧密遗传连锁的标记。     

文昌鸡神经肽Y基因多态性与开产性状的关系

[目的]检测文昌鸡神经肽Y基因（NPY）的多态性及其与开产性状的关系,为高产文昌鸡的育种提供资料。[方法]通过PCR-RFLP方法检测文昌鸡NPY基因Dra I位点上的多态性,分析其基因型、群体的遗传稳定性以及该位点多态性与开产日龄、开产体重和开产蛋重的关系。[结果]文昌鸡在NPY基因Dra I位点上有3种基因型（AA、AB、BB）;基因型的分布符合Hardy-Weinberg定律;不同基因型间的开产日龄、开产蛋重差异不显著（P〉0.05）,开产体重差异极显著（P〈0.01）。[结论]文昌鸡NPY,基因Dra I位点处于Hardy-Weinberg平衡状态,其基因多态影响开产体重。     

略阳乌鸡蛋品质分析

为研究略阳乌鸡蛋品质特性和蛋的营养价值,选取相同的玉米-豆粕型饲料饲喂的同一笼养鸡舍饲养条件下320~325日龄的略阳乌鸡、东乡乌鸡、尼克粉蛋鸡所产的鸡蛋各200枚,分别测定蛋品质指标、营养成分和蛋黄中的胆固醇、卵磷脂质量分数和脂肪酸构成比例。研究表明,(1)蛋品物理性状:略阳乌鸡蛋质量最小,且个体差异较大;蛋壳颜色一致性最差,蛋形指数最大,鸡蛋偏圆形;蛋壳厚度和蛋壳强度大于东乡乌鸡(P0.05),但小于尼克粉蛋鸡(P0.05);蛋黄色泽品种间差异不显著(P0.05);蛋白高度、哈氏单位、蛋黄与蛋白比率小于东乡乌鸡(P0.05),但大于尼克粉蛋鸡(P0.05);(2)蛋品营养物质:粗蛋白质、粗脂肪质量分数与其他品种差异不显著(P0.05);蛋黄中胆固醇质量分数显著高于其他品种(P0.05),卵磷脂质量分数品种间差异不显著(P0.05);饱和脂肪酸(SFA)的比例较高(P0.05);不饱和脂肪酸(UFA)比例较低(P0.05);单不饱和脂肪酸(MUFA)总体比例最低(P0.05);多不饱和脂肪酸(PUFA)总体的比例位于3个品种之间,与其他品种差异不显著(P0.05);距羧基最远端的双键在倒数第6个碳原子上的多不饱和脂肪酸(n-6PUFA)与距羧基最远端的双键在倒数第3个碳原子上的多不饱和脂肪酸(n-3PUFA)比值最高(P0.05)。由此说明,略阳乌鸡蛋的内部蛋品质较优,但在蛋质量、蛋壳质量和脂肪酸构成上还存在较大的改良空间。     

Association of polymorphisms in adipocyte fatty acid binding protein gene with fat-related traits in chicken

PCR-SSCP analysis was used to detect polymorphic sites in chicken adipocyte fatty acid binding protein (A-FABP) gene. Six Chinese local breeds, Beijing-You chicken, Dwarf chicken, Taihe silky chicken, Chongrenma chicken, Xiayan chicken, Luyuan chicken and an introduced foreign breed, Arbor Acre broiler, were used as test populations. Three PCR-SSCP loci were detected. Statistical results showed that frequencies of genotypes and alleles were significantly different in the test populations. Sequence analysis revealed that C → T, G → A, and C → T transitions were responsible for the polymorphisms. Some fat-related traits such as body weight, content of intramuscular fat (IMF) and percentage of abdominal fat (AFP) were measured in Dwarf chickens and male Beijing-You chickens. We found out that chicken quality was significantly related to different genotypes in these two populations. __________ Translated from Acta Veterinaria et Zootechnica Sinica, 2007, 38(6): 526–532 [译自 : 畜牧兽医学报]     

Sequencing, Polymorphism and Expression Profile Analysis of Porcine Hexokinase Ⅱ （HK2） Gene

Hexokinase Ⅱ has been demonstrated to play the role of a key enzyme member in the glycolysis reaction. It catalyzes the conversion of glucose to glucose-6-phosphate, thus committing glucose to the glycolytic pathway. In this paper, the partial exons and introns 10, 11, 13 and 14 of the porcine HK2 gene were cloned and sequenced by comparative genomics. Comparative sequencing of three pig breeds revealed ten putative single-nucleotide polymorphisms （SNPs）, one of which in intron 10 with differing bases （G981A） is within the restriction site for enzyme Msp I. Distribution of Msp I -RFLP genotype and allele frequencies among different pig breeds were studied. By association analysis between Msp I PCR- RFLP polymorphism （AA, AB, BB genotypes of HK2 gene intron 10） and some meat quality and carcass traits in F2 group, which was constructed by our laboratory, a significant difference of pig average backfat at rump was found between AB and BB genotypes （P〈0 05） in F2 group. In addition, the pattern of expression of ilK2 in a variety of tissues in pig was also determined using semi-quantitative RT-PCR. The expression of HK2 mRNA was detected only in pig skeletal muscle.     

Effect of mating combination and environmental factors on hatchability of chicken eggs in Tibet

To improve the hatchability of introduced high-yield chickens in Tibet, and ameliorate the egg yield and reproduction traits of the local Tibetan chickens, four mating combinations between the Recessive White and Tibetan chicken were employed to investigate the effect of the mating combination and environmental factors on hatchability in this study. The results showed that the fertility of the eggs with Tibetan chicken as female parent was significantly lower than that with Recessive White as female parent (P < 0.05), while hatchability was the reverse (P < 0.05). The embryonic mortality of Recessive White was significantly higher by 7.95% than the Tibetan chickens, particularly during the last stage of incubation. The hatchability of combination III, whose female parent was Tibetan chicken, was higher by 20.44% than combination II, whose female parent was Recessive White. This provided a theoretical basis for a cross using the Tibetan chicken as female parent. Binary logistic regression analysis results also showed that the mating combination and environmental temperature were of importance to egg hatchability. Translated from Acta Veterinaria et Zootechnica Sinica, 2006, 37(1): 28–33 [译自: 畜牧兽医学报]