基于SRK和SCR序列的甘蓝自交不亲和系单倍型分析

采用RT-PCR和其他分子生物学方法,以甘蓝自交不亲和系E1和F1柱头cDNA为模板扩增SRKE1和SRKF1基因,以花药cDNA为模板扩增SCRE1和SCRF1基因.经序列比对首次证明E1和F1材料分别为S28和S7单倍型.经三维结构分析,预测SCRE1上C5-C6和C7-C8之间氨基酸序列决定SCRE1的单倍型特异性,SRKE1上TNNSFYSRLKVS序列决定了SRKE1的单倍型特异性,并对两者相对作用的关键氨基酸位点进行了分析.     

禾本科8种牧草DNA条形码通用序列筛选

DNA条形码技术是利用DNA保守片段对物种进行快速准确鉴定的新兴技术。本研究根据GenBank中禾本科牧草matK和rbcL基因的核苷酸序列,设计4对通用引物,建立并优化了针对禾本科7个主要牧草属8种牧草11个样品[高丹草(Sorghum bicolor×S.sudanense)、玉米(Zea mays)、针茅(Stipa capillata)、"贝克"多年生黑麦草(Lolium perenne‘Plxie)、"凯帝莎"多年生黑麦草(L.perenne‘Caddieshack’)、甘肃羊茅(Festuca kansuensis)、"百琪"紫羊茅(F.rubra‘Bargena’)、"梦神"紫羊茅(F.rubra‘Maxima’)、"百胜"草地早熟禾(Poa pratensis‘Barvictor’)、"钻石"草地早熟禾(P.pratensis‘Diamond’)和芨芨草(Achnatherum splendens)]的目的片段的扩增条件。对扩增产物进行测序和分析,经分别比对,筛选出8种牧草的4个标记位点5’端和3’端保守序列。对各标记位点保守区内的核苷酸进行单核苷酸多态性(SNPs)的单倍型分析。结果表明,matK1、matK2、matK3分别有6个单倍型(H1~A、H1~B、H1~C、H1~D、H1~E和H1~F)、7个单倍型(H2~A、H2~B、H2~C、H2~D、H2~E、H2~F和H2~G)和3个单倍型(H3~A、H3~B和H3~C),rbcL基因有5个单倍型(H4~A、H4~B、H4~C、H4~D和H4~E)。根据matK(matK1、matK2、matK3)和rbcL基因筛选的4个标记位点为8种牧草建立了相对应的特异DNA识别码。本研究可为混合禾本科牧草饲料中的高粱属、玉蜀黍属、芨芨草属、针茅属、黑麦草属、羊茅属和早熟禾属的8种牧草准确识别提供分子水平上的科学依据。     

四川马铃薯晚疫病菌交配型、生理小种、甲霜灵敏感性 及mtDNA单倍型组成分析

【目的】对马铃薯晚疫病菌群体特征进行系统分析,为马铃薯晚疫病的防控提供科学依据。【方法】对2008—2011年采集自四川的马铃薯晚疫病菌的交配型、甲霜灵敏感性、生理小种及mtDNA单倍型进行分析。【结果】四川马铃薯晚疫病菌以A2交配型为主,占测定菌株的62.5%,A1交配型和自育型菌株的发生频率分别为18.8%和18.4%,A1交配型菌株集中在九龙县和普格县。192个菌株中共测定出55个生理小种,其中生理小种1.2.3.4.5.6.7.8.9.10.11发生频率最高,99.48%的供试菌株含有多个毒力基因。甲霜灵敏感性测定发现四川马铃薯晚疫病菌群体包含抗性、中抗和敏感菌株,分别占测定菌株的63.0%、22.0%和15.0%,敏感菌株分布于普格县、道孚县和九龙县。检测到四川马铃薯晚疫病菌有Ⅰa和Ⅱa两种单倍型,分别占测定菌株的97.4%和2.6%,为第二次全球迁移后出现的“新”群体,Ⅰa单倍型马铃薯晚疫病菌广泛分布于四川各马铃薯产区,其中存在A1交配型、A2交配型、自育型和未知交配型菌株。【结论】四川马铃薯晚疫病菌群体组成日趋复杂,亟待发掘新抗源和培育水平抗病品种,以及合理布局已有抗病品种和利用马铃薯晚疫病预警系统,科学防控马铃薯晚疫病。     

黑龙江腐烂茎线虫群体的分离和鉴定

 本研究对分离自黑龙江省马铃薯中的1个线虫群体Hp1进行形态观察与测量,采用线虫通用引物对其rDNA-ITS进行扩增与序列分析,利用PAUP软件以ML法构建系统发育树,并测定其致病性。结果显示,该线虫群体有6条侧线,头部略缢缩,口针明显,中食道球呈长纺锤形,食道峡部窄而细长;雌虫阴门稍突起,后阴子宫囊较长;雄虫交合刺略向腹面弯曲,引带短,具交合伞。其形态测量值与腐烂茎线虫(Ditylenchus destructor)基本一致。rDNA-ITS PCR扩增片段916 bp,经BLAST比对,该ITS序列与腐烂茎线虫序列相似度最高。系统发育树显示,该群体没有与腐烂茎线虫A、B基因型群体聚在一起,而是与C、D型群体聚为1个分支,且与C型亲缘关系更近。据此,将群体Hp1鉴定为腐烂茎线虫C基因型,这是首次在黑龙江省发现腐烂线虫为害马铃薯。     

甘蓝型油菜BnDMC1.A01基因的分离及序列分析

人工合成甘蓝型油菜是进行基因组学研究和种质资源创新的重要材料，但其减数分裂过程中经常出现异常，导致基因组遗传的不稳定和花粉育性的下降。DNA meiotic recombinase 1 （DMC1）是植物中控制减数分裂的重要基因，为了解油菜DMC1同源基因的序列及表达变异，本研究利用拟南芥和芸薹属作物DMC1同源基因的外显子保守序列设计引物，分离了常规和合成甘蓝型油菜（Brassica napus L.）A01染色体上的DMC1全长序列。氨基酸序列比对发现，BnDMC1.A01编码的蛋白具有植物中已报道的DMC1典型的保守结构域。分离了19个不同品系中BnDMC1.A01的基因序列，共划分为六种单倍型，发现第二外显子内存在两个导致氨基酸残基变异的SNP位点，该SNP位点在3种类型的油菜中均有分布。基因表达量分析发现，BnDMC1.A01在合成甘蓝型油菜中的表达量较常规油菜高，这些变异是否同人工合成甘蓝型油菜减数分裂异常有关还需进一步的研究验证。     

粳稻分蘖数全基因组关联分析及候选基因的挖掘

【目的】利用全基因组关联分析（genome-wide association study,GWAS）检测与粳稻分蘖数显著相关的SNP位点,筛选影响分蘖数的候选基因,为分子辅助育种提高产量提供理论基础。【方法】利用295份来自世界各地的粳稻品种,于2018和2019年分蘖盛期调查水稻分蘖数,结合高通量重测序获得的788 396个高质量多态性SNP,利用TASSEL 5.0软件的MLM模型进行全基因组关联分析,对GEC软件计算的有效独立SNP数目进行阈值确定,判定SNP标记与目标性状关联的显著性。根据2年检测到的峰值SNP和水稻每条染色体LD衰减距离,确定2年共定位分蘖数主效QTL,并进一步提取QTL区间内所有基因外显子区非同义突变SNP和启动子区SNP进行单倍型分析,结合基因注释筛选影响粳稻分蘖数候选基因。【结果】295份粳稻品种的分蘖数在2018和2019年总趋势基本一致,并且均具有较大的表型分布。通过全基因组关联分析,在P<5.46×10^-6阈值条件下,从第8、9和10染色体上共鉴定3个与粳稻分蘖数相关的QTL（qTiller8、qTiller9和qTiller10）,其中,在2年中均检测到qTiller9,在2018和2019年的表型贡献率分别为11.86%和10.61%,而qTiller8和qTiller10仅在2018年被检测到,表型贡献率分别为9.36%和9.10%。对qTiller9区间内的全部15个基因进行单倍型分析,结果表明,在qTiller9区间内共有6个基因（LOC_Os09g25090、LOC_Os09g25100、LOC_Os09g25150、LOC_Os09g25190、LOC_Os09g25200和LOC_Os09g25220）的不同单倍型分蘖数之间存在极显著差异,LOC_Os09g25090被启动子区SNP分为2种单倍型,hap2（TAA）分蘖数极显著大于hap1（AGG）;LOC_Os09g25100被非同义突变SNP分为2种单倍型,hap2（GAGA）分蘖数极显著大于hap1（AGCC）;LOC_Os09g25150被非同义突变SNP分为2种单倍型,hap2（ATG）分蘖数极显著大于hap1（GCC）;LOC_Os09g25190被启动子区SNP分为2种单倍型,hap2（GCATCGCATCGACGCCGA）分蘖数极显著大于hap1（ATGCTGATGAAGTCATCC）;LOC_Os09g25200被非同义突变SNP分为2种单倍型,hap2（TAG）分蘖数极显著大于hap1（AGA）;LOC_Os09g25220被非同义突变SNP分为2种单倍型,hap1（GG）分蘖数极其显著大于hap2（AA）。结合基因注释发现,LOC_Os09g25090和LOC_Os09g25100均预测编码钙调蛋白依赖性蛋白激酶,是脱落酸（ABA）表达所必需Ca²⁺的传感器,推测LOC_Os09g25090和LOC_Os09g25100为影响粳稻分蘖数的候选基因。【结论】筛选出LOC_Os09g25090和LOC_Os09g25100为影响粳稻分蘖数的候选基因。     

水貂ASIP基因单倍型检测及其皮肤组织mRNA差异表达分析

试验旨在探究鼠灰色（agouti signaling protein，ASIP）基因单核苷酸多态性（single nucleotide polymorphisms，SNPs）形成的单倍型及皮肤组织差异表达mRNA对水貂被毛色素沉积的影响。通过PCR扩增、Sanger测序技术对金州黑水貂、红眼白水貂和名威银蓝水貂ASIP基因进行SNPs单倍型检测分析，利用实时荧光定量PCR技术检测3种毛色皮肤组织ASIP基因的表达量，分析单倍型及mRNA差异表达与毛色表型的相关性。结果表明，301个样本中共检测到10个SNPs，内含子2中4个SNPs （G18A、A159G、G235T、C1189T）共形成10种单倍型（Hap1~Hap10），其中Hap1（GAGC）和Hap2（GAGT）是3种不同毛色水貂群体的共享单倍型；部分内含子3中6个SNPs （C252T、A290C、G298C、A340G、T343C、T379C）形成4种单倍型（Hap1~Hap4），且Hap2（CCCGCC）是名威银蓝水貂群体的主体单倍型。5个位点（A290C、G298C、A340G、T343C、T379C）均处于完全连锁不平衡状态。实时荧光定量PCR检测显示，金州黑水貂和名威银蓝水貂ASIP基因mRNA表达量分别是红眼白水貂的1.25和0.95倍，三者间差异不显著（P>0.05）。研究结果初步提示，ASIP基因调控水貂不同毛色表型形成的分子机制可能存在差异。     

Polymorphisms and haplotypes of the myostatin gene associated with growth in juvenile red sea bream Pagrus major

Polymorphisms of the myostatin gene (MSTN) have been studied in vertebrates including several aquaculture species, revealing their role in growth. We attempted to identify polymorphisms in MSTN associated with growth traits of juvenile farmed red sea bream Pagrus major, an important cultured fish species in Japan. Polymorphisms in the coding region of MSTN were screened, and six polymorphisms were found among three exons: a deletion in exon 1, a single nucleotide polymorphism (SNP) in exon 2 and four SNPs in exon 3. The deletion in exon 1 eliminated a codon (glutamine) from the region comprising the polyglutamine structure, but all SNPs were synonymous. We analysed the polymorphisms for association with growth phenotype in large and small P. major specimens obtained from commercial production at 50 days post hatching. Two SNPs located in exon 3 (c.+846T>C and c.+1140T>C) were significantly more frequent in the large group, while no SNPs were significantly associated with the small phenotype. Haplotypes were reconstructed using genotype information of the two phenotype groups, and nine haplotypes (Hap_1 to Hap_9) were successfully reconstructed. Hap_6 and Hap_7 were significantly more often observed in small and large groups respectively. Analysis of diplotypes (haplotype combinations) of individual specimens revealed 19 diplotypes. The Hap_7/Hap_7 diplotype was found in 46.7% of large phenotype specimens, significantly more frequently than in the small group (13.5%). These results will be useful for marker‐assisted selection of red sea bream to improve production with respect to growth.     

Haplotypes at the 5"-Flanking Region of Peroxisome Proliferator-Activated Receptor y Gene and Their Association with the Growth and Body Composition Traits in Chickens

Peroxisome proliferator-activated receptor y (PPARy) is an important regulator of chicken preadipocyte proliferation and differentiation. In this study, polymorphisms were detected by DNA sequencing, PCR-RFLP and some other methods and three polymorphisms (g.-1784_-1768de117, c.-1241G>A and c.-75G>A) were found in the 5' flanking region of PPARy gene.Growth and body composition traits were measured in the 8th-10th generation populations of the Northeast Agricultural University broiler lines were divergently selected for abdominal fat content. Polymorphisms among individuals were screened in the above populations. The haplotype-based association analysis on growth and body composition traits was carried out. The association analysis showed that haplotypes based on three polymorphisms at 5' flanking region of PPARy gene were significantly associated with abdominal fat weight (AFW), abdominal fat percentage (AFP, AFW/BW,),liver weight (LW), liver weight percentage (LFP, LW/BW,), shank length (ShL), femur weight (FeW), keel length (KeL), and metatarsus circle (MeC) (P<0.05) and suggestive significantly associated with pectoralis major weight (PMaW), pectoralis minor weight (PMiW), pectoralis minor weight percentage (PMiWP, PMiW/BW,), and metatarsus length (MeL) (P<0.2).The least square analysis showed that the birds with BGA haplotype had significantly higher AFW and AFP than the birds with other haplotypes (P<0.05). The birds with AAG haplotype had significantly higher LW and LW/BW than the birds with other haplotypes (P<0.05). The birds with AAG haplotype had significantly higher PMiW and PMiW/BW than the birds with other haplotypes (P<0.05). The birds with AAG haplotype had significantly higher ShL, FeW, MeL, MeC and KeL than the birds with AGG haplotypes (P<0.05). The results in this study revealed that QTL affecting fatness traits may exist in 5' flanking region of PPARy gene in chickens and PPARy gene might be one of the genes having important influences on the growth and bone traits in chickens.     

甘肃省部分地区马铃薯晚疫病菌交配型及线粒体DNA单倍型分析

由致病疫霉Phytophthora infestans(Mont.) de Bary侵染引起的马铃薯晚疫病是一种世界范围内的毁灭性病害。为了明确甘肃省马铃薯晚疫病菌的遗传结构,对2018年甘肃省定西市、张掖市和陇南市采集的130株晚疫病菌进行了交配型和线粒体DNA (mtDNA)单倍型测定。结果表明：从130株晚疫病菌中检测到A1和A2两种交配型,A1交配型为14株(10.77%),A2交配型为116株(89.23%);检测到Ⅰa、Ⅱa和Ⅱb 3种线粒体DNA单倍型,发生频率分别为88.46%、3.85%和7.69%。Ⅰa单倍型菌株的交配型为A1和A2,Ⅱa单倍型菌株交配型为A1和A2,Ⅱb单倍型菌株交配型为A1。该结果表明甘肃省部分地区马铃薯晚疫病菌以A2交配型,Ⅰa mtDNA单倍型为主。甘肃省各采集地晚疫病菌群体结构或与当地种薯繁育、调运有关。