Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations

Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase

Citation: Nestler, J., Liu, S., Wen, T. -., Paschold, A., Marcon, C., Tang, H. M., et al. (2014). Roothairless5, which functions in maize (zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase. Retrieved from krex.k-state.edu.Root hairs are instrumental for nutrient uptake in monocot cereals. The maize (Zea mays L.) roothairless5 (rth5) mutant displays defects in root hair initiation and elongation manifested by a reduced density and length of root hairs. Map-based cloning revealed that the rth5 gene encodes a monocot-specific NADPH oxidase. RNA-Seq, in situ hybridization and qRT-PCR experiments demonstrated that the rth5 gene displays preferential expression in root hairs but also accumulates to low levels in other tissues. Immunolocalization detected RTH5 proteins in the epidermis of the elongation and differentiation zone of primary roots. Because superoxide and hydrogen peroxide levels are reduced in the tips of growing rth5 mutant root hairs as compared to wild-type, and ROS is known to be involved in tip growth, we hypothesize that the RTH5 protein is responsible for establishing the high levels of ROS in the tips of growing root hairs required for elongation. Consistent with this hypothesis, a comparative RNA-Seq analysis of 6-day-old rth5 versus wild-type primary roots, revealed significant over-representation of only two gene ontology (GO) classes related to the biological functions (i.e., oxidation/reduction and carbohydrate metabolism) among 893 differentially expressed genes (FDR <5%). Within these two classes the subgroups “response to oxidative stress” and “cellulose biosynthesis” were most prominently represented

The genome of broomcorn millet

Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 proteincoding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology

Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness

Understanding the dynamics of muscle transcriptome during development and between breeds differing in muscle growth is necessary to uncover the complex mechanism underlying muscle development. Herein, we present the first transcriptome-wide longissimus dorsi muscle development research concerning Lantang (LT, obese) and Landrace (LR, lean) pig breeds during 10 time-points from 35 days-post-coitus (dpc) to 180 days-post-natum (dpn) using Solexa/Illumina's Genome Analyzer. The data demonstrated that myogenesis was almost completed before 77 dpc, but the muscle phenotypes were still changed from 77 dpc to 28 dpn. Comparative analysis of the two breeds suggested that myogenesis started earlier but progressed more slowly in LT than in LR, the stages ranging from 49 dpc to 77 dpc are critical for formation of different muscle phenotypes. 595 differentially expressed myogenesis genes were identified, and their roles in myogenesis were discussed. Furthermore, GSK3B, IKBKB, ACVR1, ITGA and STMN1 might contribute to later myogenesis and more muscle fibers in LR than LT. Some myogenesis inhibitors (ID1, ID2, CABIN1, MSTN, SMAD4, CTNNA1, NOTCH2, GPC3 and HMOX1) were higher expressed in LT than in LR, which might contribute to more slow muscle differentiation in LT than in LR. We also identified several genes which might contribute to intramuscular adipose differentiation. Most important, we further proposed a novel model in which MyoD and MEF2A controls the balance between intramuscular adipogenesis and myogenesis by regulating CEBP family; Myf5 and MEF2C are essential during the whole myogenesis process while MEF2D affects muscle growth and maturation. The MRFs and MEF2 families are also critical for the phenotypic differences between the two pig breeds. Overall, this study contributes to elucidating the mechanism underlying muscle development, which could provide valuable information for pig meat quality improvement

Experimental and theoretical study on minimum achievable foil thickness during asymmetric rolling

Parts produced by microforming are becoming ever smaller. Similarly, the foils required in micro-machines are becoming ever thinner. The asymmetric rolling technique is capable of producing foils that are thinner than those produced by the conventional rolling technique. The difference between asymmetric rolling and conventional rolling is the \u27cross-shear\u27 zone. However, the influence of the cross-shear zone on the minimum achievable foil thickness during asymmetric rolling is still uncertain. In this paper, we report experiments designed to understand this critical influencing factor on the minimum achievable thickness in asymmetric rolling. Results showed that the minimum achievable thickness of rolled foils produced by asymmetric rolling with a rolling speed ratio of 1.3 can be reduced to about 30% of that possible by conventional rolling technique. Furthermore, the minimum achievable thickness during asymmetric rolling could be correlated to the cross-shear ratio, which, in turn, could be related to the rolling speed ratio. From the experimental results, a formula to calculate the minimum achievable thickness was established, considering the parameters cross-shear ratio, friction coefficient, work roll radius, etc. in asymmetric rolling

Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations

Fabrication of ultra-thin nanostructured bimetallic foils by Accumulative Roll Bonding and Asymmetric Rolling

This paper reports a new technique that combines the features of Accumulative Roll Bonding (ARB) and Asymmetric Rolling (AR). This technique has been developed to enable production of ultra-thin bimetallic foils. Initially, 1.5 mm thick AA1050 and AA6061 foils were roll-bonded using ARB at 2006C, with 50% reduction. The resulting 1.5 mm bimetallic foil was subsequently thinned to 0.04 mm through four AR passes at room temperature. The speed ratio between the upper and lower AR rolls was 151.3. The tensile strength of the bimetallic foil was seen to increase with reduction in thickness. The ductility of the foil was seen to reduce upon decreasing the foil thickness from 1.5 mm to 0.14 mm, but increase upon further reduction in thickness from 0.14 mm to 0.04 mm. The grain size was about 140 nm for the AA6061 layer and 235 nm for the AA1050 layer, after the third AR pass

Association analysis uncovers the genetic basis of general combining ability of 11 yield-related traits in parents of hybrid rice

Association analysis between constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs) and general combining ability (GCA) effects is a novel approach to uncover the genetic basis of GCA within the sequence genomes of parents of hybrid rice. Here, we calculated the GCA effect values of 33 parents of hybrid rice and sequenced them to identify genome-wide single nucleotide polymorphisms (SNPs). In total, 64.6 % of the uniquely mapped paired-end short reads revealed a final total of 291 959 SNPs between the 33 parental genomes and the Nipponbare reference genome. The identified SNPs were non-randomly distributed among all chromosomes of rice, whereas one-fourth of the SNPs were situated in the exonic regions with 16 % being non-synonymous. Further, the identified SNPs were merged and optimized for construction of 2612 SNPLDB markers, using linkage disequilibrium information. The single-factor analysis of variance-based association method between the constructed SNPLDB markers and GCA effects values detected 99 significant SNPLDBs for GCA of 11 yield-related traits. The associated SNPLDB markers explained 26.4 % of phenotypic variations with traits, on average. We mined 50 favourable GCA alleles at the associated SNPLDBs regions, distributed across the 33 parental genomes. The parental genomes possessed a small number of favourable GCA alleles for studied traits, with the exception of days to heading and plant height. Our results suggest that the identified GCA alleles could be used to improve the GCA performance of parents of hybrid rice through optimal crossing design. Moreover, favourable GCA alleles should be incorporated in the parental genomes through marker-assisted selection experiments, and the parental lines carrying more alleles could be utilized in breeding as superior parents for developing rice hybrids of desirable characteristics

Thickness of foils for asymmetric rolling under different rolling speed ratios.

<p>Thickness of foils for asymmetric rolling under different rolling speed ratios.</p