Sampling nucleotide diversity in cotton

<p>Abstract</p> <p>Background</p> <p>Cultivated cotton is an annual fiber crop derived mainly from two perennial species, <it>Gossypium hirsutum </it>L. or upland cotton, and <it>G. barbadense </it>L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between <it>G. arboreum </it>and <it>G. raimondii</it>. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from <it>G. mustelinum </it>and <it>G. tomentosum </it>into <it>G. hirsutum </it>using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (<it>G. hirsutum</it>) × 3-79 (<it>G. barbadense</it>) have been developed to allow high-density genetic mapping of traits.</p> <p>Results</p> <p>This paper describes a strategy to efficiently characterize genomic variation (SNPs and indels) within and among cotton species. Over 1000 SNPs from 270 loci and 279 indels from 92 loci segregating in <it>G. hirsutum </it>and <it>G. barbadense </it>were genotyped across a standard panel of 24 lines, 16 of which are elite cotton breeding lines and 8 mapping parents of populations from six cotton species. Over 200 loci were genetically mapped in a core mapping population derived from TM-1 and 3-79 and in <it>G. hirsutum </it>breeding germplasm.</p> <p>Conclusion</p> <p>In this research, SNP and indel diversity is characterized for 270 single-copy polymorphic loci in cotton. A strategy for SNP discovery is defined to pre-screen loci for copy number and polymorphism. Our data indicate that the A and D genomes in both diploid and tetraploid cotton remain distinct from each such that paralogs can be distinguished. This research provides mapped DNA markers for intra-specific crosses and introgression of exotic germplasm in cotton.</p

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study the following model for population abundances in $n$ patches: the conditional law of $X_{t+dt}$ given $X_t=x$ is such that when $dt$ is small the conditional mean of $X_{t+dt}^i-X_t^i$ is approximately $[x^i\mu_i+\sum_j(x^j D_{ji}-x^i D_{ij})]dt$, where $X_t^i$ and $\mu_i$ are the abundance and per capita growth rate in the $i$-th patch respectivly, and $D_{ij}$ is the dispersal rate from the $i$-th to the $j$-th patch, and the conditional covariance of $X_{t+dt}^i-X_t^i$ and $X_{t+dt}^j-X_t^j$ is approximately $x^i x^j \sigma_{ij}dt$. We show for such a spatially extended population that if $S_t=(X_t^1+...+X_t^n)$ is the total population abundance, then $Y_t=X_t/S_t$, the vector of patch proportions, converges in law to a random vector $Y_\infty$ as $t\to\infty$, and the stochastic growth rate $\lim_{t\to\infty}t^{-1}\log S_t$ equals the space-time average per-capita growth rate \sum_i\mu_i\E[Y_\infty^i] experienced by the population minus half of the space-time average temporal variation \E[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j] experienced by the population. We derive analytic results for the law of $Y_\infty$, find which choice of the dispersal mechanism $D$ produces an optimal stochastic growth rate for a freely dispersing population, and investigate the effect on the stochastic growth rate of constraints on dispersal rates. Our results provide fundamental insights into "ideal free" movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology.Comment: 47 pages, 4 figure

Radio imaging observations of PSR J1023+0038 in an LMXB state

The transitional millisecond pulsar (MSP) binary system PSR J1023+0038 re-entered an accreting state in 2013 June in which it bears many similarities to low-mass X-ray binaries (LMXBs) in quiescence or near-quiescence. At a distance of just 1.37 kpc, PSR J1023+0038 offers an unsurpassed ability to study low-level accretion onto a highly magnetized compact object. We have monitored PSR J1023+0038 intensively using radio imaging with the Karl G. Jansky Very Large Array, the European VLBI Network and the Low Frequency Array, seeing rapidly variable, flat spectrum emission that persists over a period of six months. The flat spectrum and variability are indicative of synchrotron emission originating in an outflow from the system, most likely in the form of a compact, partially self-absorbed jet, as is seen in LMXBs at higher accretion rates. The radio brightness, however, greatly exceeds extrapolations made from observations of more vigorously accreting neutron star LMXB systems. We postulate that PSR J1023+0038 is undergoing radiatively inefficient "propeller-mode" accretion, with the jet carrying away a dominant fraction of the liberated accretion luminosity. We confirm that the enhanced ?-ray emission seen in PSR J1023+0038 since it re-entered an accreting state has been maintained; the increased ?-ray emission in this state can also potentially be associated with propeller-mode accretion. Similar accretion modes can be invoked to explain the radio and X-ray properties of the other two known transitional MSP systems XSS J12270-4859 and PSR J1824-2452I (M28I), suggesting that radiatively inefficient accretion may be a ubiquitous phenomenon among (at least one class of) neutron star binaries at low accretion rates

Effects of Chromosome-Specific Introgression in Upland Cotton on Fiber and Agronomic Traits

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic “noise” from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F(2) families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive–dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL

Genome-wide analysis of the human <it>Alu </it>Yb-lineage

<p>Abstract</p> <p>The <it>Alu </it>Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for <it>Alu </it>Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb <it>Alu </it>subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the <it>Alu </it>Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage <it>Alu </it>elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx <it>Alu </it>family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that <it>Alu </it>Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the <it>Alu </it>Yb elements will be useful in a wide range of genetic analyses.</p