Genetic Diversity and Population Structure Analysis in Early Generations Maize Inbreds Derived From Local Germplasm of Eastern Himalayan Regions Using Microsatellite Markers

North- Eastern parts of India fall under the Eastern Himalayan region and it is a diversity hotspot of many crops, including maize. Maize is an important traditional cereal crop grown in hill ecology of the region mainly for food, fodder and feed. To tap the potentiality of maize genetic resources in crop improvement programmes, assessment of genetic diversity is a basic requirement. Hence, in the present study, assessment of genetic diversity in thirty early generation maize inbreds developed from different germplasm of NE India was taken up using genome wide distributed fifty two microsatellite markers. The marker analysis revealed a large variation with a total of 189 alleles with an average of 3.63 alleles per marker locus. The allele size ranged from 50 bp ( phi 036 ) to 295 bp ( p 101049 ) which revealed a high level of genetic diversity among the loci. The PIC value ranged from 0.17 ( umc 1622 ) to 0.76 ( umc 1153 ) with an average value of 0.49. The value of expected Heterozygosity (H Exp ) ranged from 0.19 to 0.80 with an average of 0.57, whereas the Observed Heterozygosity (H Obs ) ranged from 0 to 0.89 with a mean of 0.14.The genetic dissimilarity between the genotype pairs ranged from 0.40 to 0.64 with a mean value of 0.57. Cluster analysis resolved the inbreds into three distinct sub-clusters. Similarly, population structure analysis also classified the inbred lines into three-subpopulations. Marker-trait associations showed a total of twelve SSR markers significantly associated with seven agronomic traits. From the present study, wide genetic variability was found among the maize inbreds with high potential to contribute new beneficial and unique alleles in genetic enhancement program of maize in India and particularly, in NE region.

To get sick or not to get sick—Trichomonas infections in two Accipiter species from Germany

Trichomonosis caused by the flagellate Trichomonas gallinae is one of the most important avian diseases worldwide. The parasite is localised in the oesophageal area of its host and mainly infects pigeon and dove species. During the last decade, a host expansion to passerine birds occurred, making the disease a potential threat for passerine predators as naïve host species. Here, we investigated the effect of the parasite on two Accipiter species in Germany which show a comparable lifestyle but differ in prey choice, the Northern goshawk (Accipiter gentilis) mainly hunting pigeons and the Eurasian sparrowhawk (Accipiter nisus) mainly feeding on passerines. We genetically identified the parasite strains using the Fe-Hydrogenase gene as marker locus and compared the incidence of parasite presence and clinical signs of trichomonosis between nestlings of the two Accipiter species. In total, we identified 14 strains, with nine strains unknown so far. There was a higher strain diversity and prevalence of Trichomonas spp. in goshawks than sparrowhawks (42.4% vs. 21.2%) whereas sparrowhawks when being infected more often displayed clinical signs of trichomonosis than goshawks (37.1% vs. 6.1%). Even though sparrowhawks were mainly infected with the finch epidemic strain and genetic data indicated some variation between isolates, no correlation with virulence could be detected. All in all, goshawks seem to be better adapted to Trichomonas infections, whereas to sparrowhawks, this is a novel disease with more severe manifestations, from individual morbidity to a higher risk of population decline caused by trichomonosis.

Association analysis between Lipoxygenase activity and SSR markers in wheat grains

Lipoxygenase (LOX) activity is closely related to wheat processing and storage quality. In the present research, ten wheat cultivars were used to compare the effects of genotype, location, year, and their interactions on the LOX activity. Furthermore, 123 wheat cultivars were evaluated for LOX activity with 192 simple sequence repeat (SSR) markers and to identify elite alleles related to LOX activity. The results indicated that LOX activity was highly affected by genotype (variety) than that by the location. A total of 22 SSR molecular marker loci with a significant or very significant correlation with LOX activity were identified on performing association analysis. In 3 years, only one molecular marker locus associated with LOX activity was detected (WMC488); in 2 years, seven molecular marker loci were detected, while in only 1 year, the other 14 molecular marker loci were detected. A total of 7 and 6 marker loci significantly related to LOX activity accounting for 31.2% and 27.2%, respectively, were located in homologous groups 4 and 5, and group 7. This research provided the theoretical basis and the markers for molecular-assisted wheat breeding that facilitate the breeding process in the processing and storage quality of grains.

Field resistance and molecular detection of the orange rust resistance gene linked to G1 marker in Brazilian cultivars of sugarcane

ABSTRACT Sugarcane (Saccharum spp.), an important crop for tropical and subtropical countries, is used in the production of sugar and biofuel. Orange rust, a disease caused by the fungus Puccinia kuehnii, can reduce the yield and harm the sugarcane industry. Molecular markers linked to resistance genes can help breeding programs confirm introgression of favorable alleles, find new resistance sources and release new cultivars that have durable resistance. In the current study, the aims were (i) to evaluate in the field the resistance to orange rust of 24 Brazilian commercial cultivars; (ii) to assess the frequency of the allele at G1 marker locus in the set of cultivars, and (iii) to study the usefulness of G1 marker to predict the resistant phenotype and its potential for marker assisted selection. A diagrammatic scale, which ranged from 1 (plants without symptoms) to 9 (highly susceptible plants), was used to determine the disease severity. Considering resistant cultivars those with mean severity up to 3, G1 marker efficiency in predicting the resistant phenotype was 71.43%. In addition, there was a reduction of 35% in the overall mean severity when G1 marker was present. G1 marker is an important molecular tool that can be used by breeding programs in the search for sugarcane cultivars resistant to orange rust.

High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL™ software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae.

Association mapping of germinability and seedling vigor in sorghum under controlled low-temperature conditions

Sorghum is one of the world’s most important food, feed, and fiber crops as well as a potential feedstock for lignocellulosic bioenergy. Early-season planting extends sorghum’s growing season and increases yield in temperate regions. However, sorghum’s sensitivity to low soil temperatures adversely impacts seed germination. In this study, we evaluated the 242 accessions of the ICRISAT sorghum mini core collection for seed germination and seedling vigor at 12 °C as a measure of cold tolerance. Genome-wide association analysis was performed with approximately 162 177 single nucleotide polymorphism markers. Only one marker locus (Locus 7-2) was significantly associated with low-temperature germination and none with vigor. The linkage of Locus 7-2 to low-temperature germination was supported by four lines of evidence: strong association in three independent experiments, co-localization with previously mapped cold tolerance quantitative trait loci (QTL) in sorghum, a candidate gene that increases cold tolerance and germination rate when its wheat homolog is overexpressed in tobacco, and its syntenic region in rice co-localized with two cold tolerance QTL in rice. This locus may be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.

Linkage Analysis and Map Construction in Genetic Populations of Clonal F1 and Double Cross

In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, then Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Traveling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F1. Once the four haploids were built, clonal F1 hybrids could be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F1 populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap, and R/qtl show that the methodology proposed in this article can build more accurate linkage maps in less time.

Genetic polymorphism of fifteen microsatellite loci in Brazilian (blue-egg Caipira) chickens

The purpose of this study was to investigate the genetic polymorphism of fifteen microsatellites loci in Brazilian (blue-egg Caipira) chickens. Samples were collected from 100 blue eggs of Caipira chickens from rural properties in the city of Dois Lajeados, RS. After DNA extraction, the fragments related to molecular markers LEI0248, LEI0221, LEI0214, LEI0192, LEI0217, LEI0254, LEI0194, LEI0212, MCW0371, ADL0278, LEI0234, MCW0183, MCW0216, MCW0330 and MCW0081 were obtained by polymerase chain reaction (PCR). The statistical analysis were carried out with the softwares ARLEQUIN 3.5 version and CERVUS 3.0.3 version. The allelic and genotypic frequencies, deviations from Hardy-Weinberg equilibrium, estimates of observed (HO) and expected (HE) heterozygosity and polymorphic information content (PIC) were obtained for each marker locus. A total of 186 alleles from 15 loci were obtained, with sizes ranging of 83 to 490 base pairs. The medium number of alleles was 12.4, the HE was 0.76±0.14 and HO was 0.49±0.21 and PIC was 0.706. The first conclusion is that the microsatellites used are polymorphic and can be used to genetic studies in chickens. The second is that the "Caipira" chicken (blue eggs) population investigated has a great genic variability, which makes than an important source of genetic resources for future animal breeding programs.