Application of SolCAP Genotyping in Potato (Solanum tuberosum L.) Association Mapping.

Potato variety development entails a number of breeding steps, as well as testing and, finally, commercialization. Historically, phenotypic assesment were carried out to select and germplasm development. The US Department of Agriculture (USDA) funded the Solanaceae Coordinated Agricultural Project (SolCAP) to decode genomic resources into tools that breeders and geneticists can use. This project resulted in the creation of a genome-wide single-nucleotide polymorphism (SNP) array that can be used to evaluate elite potato-breeding germplasm. This array was used to genotype a diverse panel of Solanum species, as well as numerous biparental, diploid, and tetraploid populations. It has high marker density to generate genetic maps that can be used to identify numerous quantitative trait loci (QTLs) for agronomic, quality, biotic, and abiotic resistance traits. Up to now, numerous QTLs for important traits have been identified using new diploid and tetraploid genetic maps. SNP markers were used to assess germplasm relationships and fingerprint varieties and identify candidate genes. The Infinium 8303 SolCAP Potato array offers a common set of SNP markers that can be used for mapping, germplasm assessment, and fingerprinting with confidence. This array has also been helpful in furthering our understanding of the potato genome. Furthermore, some other Infinium potato arrays (i.e., 12 K, 20 K, and 25 K) have been genotyped, and breeders can map quantitative trait loci (QTLs) across multiple populations to improve our understanding of economically important traits and lead to marker-assisted selection (MAS) and breeding and, ultimately, improved varieties.

An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice).

There is a significant interest while utilizing association mapping technique to determine the genes which are accountable for numerical dissimilarity of the more complex characteristics with agronomic and evolutionary significance. Recently improvements have been made in genomic technology, which motivates for the exploitation of natural diversity, and establishment of more vigorous and strong statistical analysis methods. It creates association mapping technique more demanding and reasonable to plant research programs. Genome-wide association mapping technique recognizes quantitative trait loci (QTLs) by studying the marker-trait associations which could be credited to the power of linkage disequilibrium between different molecular markers and functional polymorphisms through a pool of diversified germplasm. In this review, we will describe an overview of genetic mapping and the current status of association mapping studies in model cereal crops i.e., wheat and rice.

Genome-wide analysis of bZIP, BBR, and BZR transcription factors in Triticum aestivum.

Transcription factors are regulatory proteins known to modulate gene expression. These are the critical component of signaling pathways and help in mitigating various developmental and stress responses. Among them, bZIP, BBR, and BZR transcription factor families are well known to play a crucial role in regulating growth, development, and defense responses. However, limited data is available on these transcription factors in Triticum aestivum. In this study, bZIP, BBR, and BZR sequences from Brachypodium distachyon, Oryza sativa, Oryza barthii, Oryza brachyantha, T. aestivum, Triticum urartu, Sorghum bicolor, Zea mays were retrieved, and dendrograms were constructed to analyze the evolutionary relatedness among them. The sequences clustered into one group indicated a degree of evolutionary correlation highlighting the common lineage of cereal grains. This analysis also exhibited that these genes were highly conserved among studied monocots emphasizing their common ancestry. Furthermore, these transcription factor genes were evaluated for envisaging conserved motifs, gene structure, and subcellular localization in T. aestivum. This comprehensive computational analysis has provided an insight into transcription factor evolution that can also be useful in developing approaches for future functional characterization of these genes in T. aestivum. Furthermore, the data generated can be beneficial in future for genetic manipulation of economically important plants.

Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel.

Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Nigde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.

Mobile genomic element diversity in world collection of safflower (Carthamus tinctorius L.) panel using iPBS-retrotransposon markers.

Safflower (Carthamus tinctorius L.) is a multipurpose crop of dry land yielding very high quality of edible oil. Present study was aimed to investigate the genetic diversity and population structure of 131 safflower accessions originating from 28 different countries using 13 iPBS-retrotransposon markers. A total of 295 iPBS bands were observed among which 275 (93.22%) were found polymorphic. Mean Polymorphism information content (0.48) and diversity parameters including mean effective number of alleles (1.33), mean Shannon's information index (0.33), overall gene diversity (0.19), Fstatistic (0.21), and inbreeding coefficient (1.00) reflected the presence of sufficient amount of genetic diversity in the studied plant materials. Analysis of molecular variance (AMOVA) showed that more than 40% of genetic variation was derived from populations. Model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 131 safflower accessions into four main populations A, B, C, D and an unclassified population, with no meaningful geographical origin. Most diverse accessions originated from Asian countries including Afghanistan, Pakistan, China, Turkey, and India. Four accessions, Turkey3, Afghanistan4, Afghanistan2, and Pakistan24 were found most genetically distant and might be recommended as a candidate parents for breeding purposes. The findings of this study are most probably supported by the seven similarity centers hypothesis of safflower. This is a first study to explore the genetic diversity and population structure in safflower accessions using the iPBS-retrotransposon markers. The information provided in this work will therefore be helpful for scientists interested in safflower breeding.