Model averaging for genome‐enabled prediction with reproducing kernel Hilbert spaces: a case study with pig litter size and wheat yield

Predictive ability of yet‐to‐be observed litter size (pig) grain yield (wheat) records of several reproducing kernel Hilbert spaces (RKHS) regression models combining different number of Gaussian or t kernels was evaluated. Predictive performance was assessed as the average (over 50 replicates) predictive correlation in the testing set. Predictions from these models were combined using three different types of model averaging: (i) mean of predicted phenotypes obtained in each model, (ii) weighted average using mean squared error as weight or (iii) using the marginal likelihood as weight. (ii) and (iii) were obtained in a validation set with 5% of the data. Phenotypes consisted of 2598, 1604 and 1879 average litter size records from three commercial pig lines and wheat grain yield of 599 lines evaluated in four macro‐environments. SNPs from the PorcineSNP60 BeadChip and 1447 DArT markers were used as predictors for the pig and wheat data analyses, respectively. Gaussian and univariate t kernels led to same predictive performance. Multikernel RKHS regression models overcame shortcomings of single kernel models (increasing the predictive correlation of RKHS models by 0.05 where 3 Gaussian or t kernels were fitted in the RKHS models simultaneously). None of the proposed averaging strategies improved the predictive correlations attained with single models using multiple kernel fitting.     

Characterization of nonautonomous Tc1-like transposable elements of channel catfish (Ictalurus punctatus)

Putative nonautonomous transposable elements from channel catfish (Ictalurus punctatus) were identified. They were named Tipnon elements for Tc1-like transposable elements from channel catfish that are nonautonomous. These elements were defined by their terminal repeats that share identity to members of the known Tc1/mariner transposon superfamily. They show structural similarities to Tc1-like elements, but share little sequence identity beyond the terminal inverted repeats. They do not harbor any amino acid blocks that show similarities to the Tc1-like or other transposases and thus may represent truly nonautonomous transposons in channel catfish. They are abundant in the channel catfish genome with a copy number of 32000, having 500 base pair per copy, this family of nonautonomous transposon-like elements account for 1.6% of the channel catfish genomic DNA. Their high abundance and transposon-like terminal repeats indicate that they may play important roles in gene evolution and in genomic architecture of catfish. Similarity search for potential coding capacity of the Tipnon elements revealed that they contain sequence blocks that can potentially encode amino acid blocks similar to the para-type sodium channel proteins in cockroaches or house flies, proteins that function in the central nervous system as voltage-gated sodium transporters. Sequences surrounding the terminal inverted repeats are divergent from those used by the reconstructed Sleeping Beauty fish transposase.     

番鸭细小病毒和鹅细小病毒生化及基因组特性的比较

番鸭细小病毒莆田株（MPV-P）和鹅细小病毒莆田株（GPV-P）分别感染的番鸭胚尿囊液经氯仿处理、PEG沉淀和Sepharose4B柱纯化。纯化样品在电镜下观察，均见到实心和空心2种病毒粒子。病毒粒子呈圆形，立体对称，无囊膜，直径为20-24nm。经SDS-PAGE分析，MPV和GPV均呈现3条结构蛋白带。MPV结构蛋白的相对分子质量约为VP1 89000、VP2 78000和VP3 61000，其中VP3为主要结构蛋白。GPV要相对分子质量与MPV有微小差别。MPV和GPV核酸均为单链DNA，长度约为51000bp。分别以MPV核酸和GPV核酸为模板，加到无引物的DNA聚合酶Ⅰ大片段合成体系中，合成产物经1%琼脂糖凝胶电泳，均可见长度约为5600bp的双链DNA带，证明MPV和GPV核酸的3'末端具有发夹结构。对这2种病毒核酸及经Klenow合成的双链核酸进行限制性内切酶分析，两者的酶切结果明显不同，表明MPV和GPV核酸在一级结构上存在明显差异。以上结果证明，MPV和GPV不但在致病性上有显著养异，而且在核酸结构上也有明显差异。     

Genomic constitutions and flower characteristics of selected Aranda orchid cultivars

Summary Ten Aranda cultivars commercially grown in Singapore were selected to study their genomic constitutions and flower characteristics. Cytological evidence and breeding records of these cultivars showed that they are of three genomic classes. Four of them are diploid with AV genomes (one Arachnis and one Vanda genome), another four are triploid with AVV genomes and the remaining two are tetraploid with AVVV genomes. Sizes of flowers as well as of sepals and petals generally show significant increases from diploid to tetraploid. This trend reflects the increasing influence of Vanda resulting from additional one and two Vanda genomes in triploid and tetraploid respectively as compared to diploid cultivars. Among the three genomic classes, diploid cultivars generally bear less flowers per spray than those of triploid and tetraploid although exceptions may occur. There is no clear trend in the length of inflorescences although diploid cultivars tend to have less compact spray with flowers more distantly spaced out.     

Tan-Spot Resistance Screening of Aegilops Species

Two hundred and twelve accessions of 8 diploid and 10 polyploid species of Aegilops were evaluated for resistance to tan-spot disease of wheat, caused by Pyrenophora tritici-repentis (Died.) Drechs., under greenhouse conditions. One or more accessions of Ae. bicornis, Ae. biuncialis, Ae. Crassa, Ae. columnaris, Ae. cylindrica, Ae. speltoides, Ae. squarrosa. Ae. triaristata. Ae. triuncialis, and Ae. Ovata showed resistance following a 24-hour post-inoculation wet period. With a 36-hour wet period, diploids became only slightly or moderately susceptible and resistant polyploids became susceptible. A 48-hour wet period resulted in still greater susceptibility of both diploid and polyploid species.     

Occurrence of 2n gametes in the F1 hybrids of Oriental × Asiatic lilies (Lilium): Relevance to intergenomic recombination and backcrossing

Cytological modes of the origin of 2n gametes were investigated in six different genotypes of F₁ hybrids between Oriental and Asiatic (OA) lilies (Lilium, 2n = 2x = 24). Chromosome pairing between the parental genomes was very low, the average frequency range from 0.3 to 1.2 bivalents per cell among the genotypes. Within a genotype the frequency of bivalents varied from 0 to 6 in some cases. The normally occurring haploid pollen grains were totally sterile. In contrast, in different genotypes, variable percentages of 2n pollen were found and shown to be fertile as estimated from pollen germination. A cytological analysis of Metaphase I and subsequent stages of meiosis using genomic in situ hybridization (GISH) revealed that there was intergenomic recombination between the alien genomes. Following Metaphase I stage, three different types of abnormal cytological events led to the formation of 2n pollen: (i) Post-Metaphase I division (PMI), (ii) Post-Metaphase II division (PMII) and (iii) Asymmetric Cytokinesis of the pollen mother cell followed by chromosome division. All three cytological events led to first division restitution (FDR) gametes. Based on in vitro pollen germination it was proved for two genotypes that 2n pollen was viable only during the first day of anthesis. It was possible to use 2n pollen successfully for backcrossing. Implications of 2n pollen for intergenomic recombination in BC₁ progenies are discussed.     

莴苣花叶病毒北京分离物基因组3′末端序列分析

笔者通过RT-PCR方法对LMV北京分离物（LMV-BJ）基因组3＇端1620nt的核苷酸片段进行了克隆和序列分析（GenBank登录号为EF423619）。所获片段含有NIb基因3＇端的574nt,编码NIb C-端190个氨基酸;完整的CP基因,全长为834nt,编码一个由277个氨基酸组成的分子量约为30kDa的结构蛋白;3＇非编码区含有209nt。通过序列分析软件将LMV-BJ与已经报道的法国分离物O（X97704）、法国分离物E（X97705）,美国分离物（X65652）,巴西分离物（AJ278854）和余杭分离物（AJ306288）基因组3＇末端和CP基因的核苷酸序列与氨基酸序列分别进行了比较。     

Variation of the genomic proportion of the recurrent parent in BC1 and its relation to yield performance in sorghum (Sorghum bicolor) breeding for low-input conditions

In order to define the variation of the genomic proportion of the recurrent parent [G(RP)] and its relation to yield, G(RP) of individual BC₁ plants of two sorghum populations composed of a high‐yielding cultivar as recurrent parent (RP) and a donor with superior drought resistance or grain quality, respectively, was estimated using AFLPs and SSRs. G(RP) in BC₁ ranged from 0.53 to 0.95 and averaged to 0.76 in the population (NP4453 × ‘SV‐2’) × ‘SV‐2’. G(RP) varied between 0.60 and 0.86 and averaged to 0.74 in the BC₁ of (ICV‐219 × ‘SV‐2’) × ‘SV‐2’. Results show that plants with a G(RP) equivalent to BC₂ (0.875) or BC₃ (0.938), respectively, can be selected from BC₁. Yield performance of BC₁S₁ families was tested in field trials carried out in South Africa. The correlation between yield and G(RP) in BC₁ was low. Selection according to G(RP) did not result in an effective preselection for yield.     

琼氏不动杆菌GXP04的苯酚羟化酶基因的克隆及序列分析

提取琼氏不动杆菌GXP 04的总DNA,采用限制性内切酶E coRⅠ酶切处理后,构建以pLAFR 3为载体的基因组文库。通过TA IL-PCR扩增出苯酚羟化酶的上游基因,对菌落原位杂交获得的11个转化子进一步鉴定,最终确定其中的8个转化子含有完整的苯酚羟化酶基因,选取其中的pLAFR 3-7对GXP 04的苯酚羟化酶基因的核苷酸序列进行分析,并对其蛋白质基本性质进行预测。     

利用基因芯片技术筛选棉纤维伸长相关基因

从回交近交系(backcross inbred lines, BIL)群体中选取纤维长度差异较大的两个系NMGA-062 (33.03 mm)和 NMGA-140 (25.87 mm),利用Affymetrix棉花基因芯片,分析其开花后10 d (DPA, days post anthesis)棉纤维伸长相关基因表达谱。在24 029条转录本中,两材料间差异表达的转录本有7 282条,占总数的30.31%;其中差异表达倍数在2倍或2倍以上的转录本有3 993条,占筛选转录本总数的16.62%,功能分类表明这些转录本主要包括功能预测基因(15.57%)、翻译、核糖体结构相关基因(13.54%)和翻译后修饰、蛋白质转换相关基因(9.29%)3大类。为了验证芯片数据的可信性,8个差异表达显著的基因(Ghi.10655.1.S1_s_at, ACO1, ARF1, SAHH, TUA6, TUA7, β-tub1, β-tub10)被用于实时荧光定量PCR。两种检测手段表现出一致性。随后,利用实时荧光定量PCR对3个与棉纤维相关基因(ARF1, β-tub1, β-tub10)在纤维发育不同时期(5、10、15、20和25 DPA)的表达模式进行了研究,结果表明,3个基因在纤维伸长发育时期(10和15 DPA)大量表达,推测这3个基因可能与棉纤维伸长有重要关系。