Unstable Allotetraploid Tobacco Genome due to Frequent Homeologous Recombination, -. Segmental Deletion, and Chromosome Loss

The types of mutations and their corresponding frequencies are difficult to measure in complex genomes. In this study, a high-throughput method was developed to identify spontaneous loss-of-function alleles for the resistance gene N and the transgenic avirulence gene P50 in allotetraploid tobacco. A total of 2134 loss- of-function alleles of the N gene were identified after screening 14 million F1 hybrids. Analysis of these mutants revealed striking evolutionary patterns for genes in polyploids. Only 14 of the loss-of-function mutations were caused by spontaneous point mutations or indels, while the others were caused by home- ologous recombination （with a frequency of 1/12 000） or chromosome loss （1/15 000）. Loss of the chromosome with the PS0 insertion occurred at a similar frequency （1/13 000）, and the frequency of spon- taneous segmental deletion in this chromosome was 1/16 000. Both homeologous recombination and chromosome loss considerably decreased the viability of the mutants. Our data suggest that the high mutation rate in polyploids is probably due to the occurrence of homeologous recombination and the toler- ance of large mutations such as chromosome loss in polyploid genomes. Frequent mutations tend to drive polyploids to extinction unless a novel mutation helps the polyploid to effectively compete with diploids or find a new ecological niche.

三峡库区黄土坡临江滑坡体水岩(土)相互作用机理

水岩(土)相互作用与滑坡地质灾害的形成密切相关。选取仍处于变形阶段的三峡库区黄土坡临江滑坡体为研究对象,以从滑坡不同部位采集的8类滑坡不良地质体(包括滑带土、软弱层、软岩等)为研究样本,追踪测试各样本的矿物类型及含量、化学组分及颗粒级配等指标。经分析,各类不良地质体之间具有明显的同源性特征,在水岩(土)相互作用下,主要滑坡不良地质体的成因及转化过程得以清晰呈现。随后,另取主滑带附近垂直方向上的岩土体样本为例,结合试验数据,深入分析并直观展现了水岩(土)相互作用对岩土体微观结构和力学性能弱化的影响。本研究深入探讨了黄土坡临江滑坡体中的水岩(土)相互作用机理,研究成果对于了解相似滑坡灾害的形成过程和有针对性制定滑坡防治方案具有重要参考价值。

利用分子标记将2Ai-2染色体转移到小麦ph1b遗传背景的研究

小麦ph1b突变体可诱导部分同源染色体配对和交换,产生遗传上较为稳定、补偿性较好的重组体。将外源染色体引入ph1b的小麦遗传背景是产生目标染色体重组体的基础,但ph1b植株没有明显而稳定的表型性状,难以从表型上进行选择。本研究利用CSph1b缺失区中的分子标记Mads及外源染色体特异的分子标记P4和P68,对小麦-中间偃麦草2Ai-2(2B)异代换系N420与CSph1b的杂种F2群体及其衍生的F5株系进行ph1b-2Ai-2染色体综合体的选择,高效地获得了目标基因型。

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

Cloning of TaCYP707A1 Gene that Encodes ABA 8′-Hydroxylase in Common Wheat (Triticum aestivum L.)

The plant hormone abscisic acid （ABA） regulates many important physiological and developmental processes in plants. The objective of this study was to clone the ABA 8′-hydroxylase gene in common wheat. In the present study, we used the eDNA sequence of barley HvCYP707A1 gene （GenBank accession no. AB239299） as a probe for BLAST search against the common wheat （Triticum aestivum L.） EST database in GenBank. All wheat ESTs sharing high similarity with the reference gene were subjected to contig assembly. Primers were designed based on the constructed contigs to clone the wheat CYP707A1 gene, designated as TaCYP707A1. The genomic DNA sequence of TaCYPTO7A1 gene comprised five exons and four introns, with a size of 2225 bp. The corresponding cDNA sequence of TaCYP707A1 was 1737 bp, containing an open reading frame （ORF） of 1431 bp, a 42-bp 5′-untranslated region （UTR） and a 264-bp 3′UTR, with 94.9% of identical sequences to HvCYP707A1 gene （AB239299）. The neighbor joining tree indicated that the deduced amino acid sequences of TaCYP707A1 gene was highly similar to those of barley and rice. The TaCYP707A1 gene was located on chromosome 6BL using a set of Chinese Spring nullisomic-tetrasomic lines and ditelosomic line 6BS. These results will be of high importance in understanding of molecular mechanism of ABA catabolism.

Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq

Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations;however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

普通高校武术专业开设书法课程的价值探析

随着武术在世界范围内的推广与发展,武术的防身功用、健身价值、文化意义越来越被人们所重视,武术人才尤其是武术专业教师、教练员的需求量增大,其培养工作意义重大。以书法艺术与武术的相互联系为切入点,分析两者在技艺学习过程中的相辅相成的相通之处,探讨普通高校武术专业课程中开设书法课程的价值和意义,以期为普通高校武术专业人才培养提供参考。

Single Nucleotide Polymorphism Identification in Polyploids： A Review, Example, and Recommendations

Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.

Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing

Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed ＂transcriptome shock＂. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica （2n=2x=24, genome AA） and the tetraploid form of O. punctata （2n=4x =48, genome, BBCC）, and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico ＂hybrids＂ （parental mixtures）. We found that approximately 16% （2,541） of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the tran- scriptome response to interspecific hybridization and heterosis.

高原藜米(Chenopodium quinoa Willd.)单基因性状的异源四倍体分离现象

高原藜米(Chenopodium quinoa Willd.)是一个异源四倍体作物,但有些研究报道该作物在单个基因位点上的分离行为有二倍体分离特征。本研究在多年观察试验的基础上,2011-2012年两年在西藏不同海拔(南木林县:海拔4 000 m;林芝:海拔2 800 m)条件下对雄性不育植株进行杂交所得的F1和F2代中分离产生了3种不同的单基因控制的性状特征进行了较大群体的观测试验。等位基因分离分析结果显示,在F1和F2的分离范围内出现了二体双基因和四体的遗传性状,在F2代减数分裂中出现的一定比例的畸变现象也显示了其不定的多价体形态,这些结果都表明了藜米的异源四倍体特征。这一特征产生的根本原因是某些基因位点重复和至少在有些同源染色体之间发生了联会现象。本研究发现,藜米某些基因位点发生的四倍体分离现象可能导致了藜米育种和遗传研究中的复杂性,对于指导该作物育种或生产都有一定的实际意义。四倍体分离,特别是其飘忽不定的现象,可能会使将来藜米基因图谱研究分析变的更加复杂,这一点在今后的研究中应给予足够的重视。