Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

<p>Abstract</p> <p>Background</p> <p>A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (<it>Triticum aestivum</it>, genomes AABBDD) and wild tetraploid wheat (<it>Triticum turgidum </it>ssp. <it>dicoccoides</it>, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.</p> <p>Results</p> <p>Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, <it>T. urartu</it>, <it>Aegilops speltoides</it>, and <it>Ae. tauschii</it>, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an <it>Ae. tauschii </it>genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.</p> <p>Conclusions</p> <p>In a young polyploid, exemplified by <it>T. aestivum</it>, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in <it>T. aestivum </it>is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.</p

Ibigkas!: The Iterative Development of a Mobile Collaborative Game for Building Phonemic Awareness and Vocabular

Filipino learners’ lack of English language proficiency is a major barrier to higher education opportunities and participation in high-value industries. Computer-based learning systems have the potential to increase educational quality, equity, and efficacy in the Global South. However, a key challenge is to design systems that are developmentally and socioculturally appropriate and engaging for the target learners. In this paper, we describe the design, development, and preliminary testing of Ibigkas!, a collaborative, mobile phone-based game designed to provide phonemic awareness and vocabulary building support to Filipino learners aged 10-12

Analyzing Online Protocols to Characterize Novice Java Programmers

Computer science educators are concerned and disappointed over students’ lack of programming comprehension. This concern has motivated investigations into areas that programming students do not understand, in an effort to provide students with the foundation they need in order to produce correct software. In this study, we built and used several tools to study the behavior of novice programmers—what edits they make, when they compile their programs, and how they respond to errors. The characterization enables computer science educators to identify at-risk students and determine specific interventions. These tools include summarization of student compilation errors, computation of time between compilations, computation of Error Quotients, and a browser that enables educators to view successive compilations. This paper describes how these tools are used and what implications educators can infer from the data that they present

Affective and behavioral predictors of novice programmer achievement

We study which observable affective states and behaviors relate to students\u27 achievement within a CS1 programming course. To this end, we use a combination of human observation, midterm test scores, and logs of student interactions with the compiler within an Integrated Development Environment (IDE). We find that confusion, boredom and engagement in IDE-related on-task conversation are associated with lower achievement. We find that a student\u27s midterm score can be tractably predicted with simple measures such as the student\u27s average number of errors, number of pairs of compilations in error, number pairs of compilations with the same error, pairs of compilations with the same edit location and pairs of compilations with the same error location. This creates the potential to respond to evidence that a student is at-risk for poor performance before they have even completed a programming assignment

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere–telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere–telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae. tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere–telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated