P. Kadirvel

Using SSR markers to map genetic diversity and population structure of Solanum pimpinellifolium for development of a core collection

The present study was undertaken to examine the population structure of the Solanum pimpinellifolium collection maintained by AVRDC – The World Vegetable Center – and to construct a core set of this collection. Out of the entire collection of 322 accessions, a diverse subset of 190 accessions was chosen representing 14 countries of origin. Data on 32 qualitative and 22 quantitative phenotypic traits (IPGRI–AVRDC descriptor traits) and 48 simple sequence repeat markers evenly distributed over the genome were used to develop the core set. A total of 377 alleles were detected with 7.85 alleles per locus, on average. Of these, 52 alleles at 28 loci were extremely rare-frequency alleles. The 190 accessions clustered into two main populations and an admixture group. Population I (PopI) included 99 accessions, 93 of which originated from Peru. Population II (PopII) contained 49 accessions, the majority of which originated from Ecuador and Mexico. The remaining 42 accessions were classified as admixture group. The two main populations were further subdivided into five subgroups. Values of Fst among the five sub-populations were significant (average pairwise Fst of 0.296), suggesting a real difference between these populations. A clear differentiation was observed among and within populations based on geography. Peruvian accessions were genetically more diverse than accessions originating in Ecuador and Mexico. Within the Peruvian group, a gradual increase in genetic diversity was observed from southern to northern Peru. The constructed core collection consists of 75 accessions representing 23.4% of AVRDC’s entire S. pimpinellifolium collection and 39.5% of the subset used in this study. It is a well-balanced core with a good representation of the different populations (31 accessions from PopI, 22 from PopII and 22 from the Admixture group) and geographic origins (40 accessions from

Application of Cytochrome Oxidase I Sequences for Phylogenetic Analysis and Identification of Thrips Species Occurring on Vegetable Crops

ABSTRACT Thrips are direct pests as well as vectors of important viruses infecting crop plants. One of the major constraints in studying the relationship between thrips vectors and tospoviruses is the difficulty of identifying the vector species because of high intraspecific variation among thrips populations. Molecular approaches have been used to identify species differences. In this study, partial cytochrome oxidase I (COI) sequences were used to understand the phylogenetic relationship among thrips populations, and assess their usefulness to identify and classify unknown thrips species collected from different crops. In total, 29 COI variants were obtained while examining the sequence polymorphisms in COI of 182 insects analyzed in this study, which were collected from six countries on tomato, chilli, onion, cabbage, cucumber, watermelon, Ethiopian mustard, French bean, and peanut. The phylogenetic analysis showed that the insects used in this study clustered with five distinct species-groups designated as Thrips palmi group, T. tabaci group, Frankliniella occidentalis group, Scirtothrips dorsalis group and an unclassified group. Higher intraspecific genetic variation was observed in S. dorsalis and T. palmi followed by T. tabaci and F. occidentalis. Thus, it was confirmed that the COI gene could be useful in grouping different thrips species and genera that coexist in a particular cropping system.

Relationship between survival and yield related traits in Solanum pimpinellifolium under salt stress

A subset of the Solanum pimpinellifolium collection maintained by AVRDC—The World Vegetable Center, Taiwan was evaluated to assess effects of salt stress on physiological traits and yield-related traits with the aim of identifying potential S. pimpinellifolium accessions useful for salt tolerance breeding in tomato. We undertook a comparative analysis of yield and plant survival traits under normal and salt stress conditions to obtain a first indication of the crucial traits associated with salt tolerance in S. pimpinellifolium. Although most traits of S. pimpinellifolium accessions showed a similar percent decrease in mean under salt stress compared with the cultivated checks, the former exhibited a wide range for all traits, suggesting great genetic diversity that can be exploited for the identification of salt tolerant genotypes. Genetic variability for yield and survival traits under salt stress was quantitative with low to moderate heritability. Results of correlation and path coefficient analysis revealed no correlation between any of the physiological traits with yield-related traits indicating that the ability to survive and yield under salt stress are two independent sets of traits in S. pimpinellifolium. Results of the path analysis along with heritability and genetic advance showed that shoot dry weight and K/Na ratio are the two most critical component traits for survival, while fruit number is critical for yield per plant. The large S. pimpinellifolium panel evaluated in this study revealed five genotypes possessing better survival traits, seven genotypes with good yield traits, and two genotypes combining both superior survival and yield traits under salt stress.

Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium)

Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0% to 25.8% phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A_297_6 and SpDREB1A_297_12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten marker-assisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato.

Genetic Markers, Trait Mapping and Marker-Assisted Selection in Plant Breeding

Genetic markers have long been used for characterization of plant genetic diversity and exploitation in crop improvement. The advent of DNA marker technology (during 1980s) has revolutionized crop breeding research as it has enabled the breeding of elite cultivars with targeted selection of desirable gene or gene combinations in breeding programmes. DNA markers are considered better over traditional morphology and protein-based markers because they are abundant, neutral, reliable, convenient to automate and cost-effective. Over the years, DNA marker technology has matured from restriction based to PCR based to sequence based and to eventually the sequence itself with the emergence of novel genome sequencing technologies. Trait mapping has been the foremost application of molecular markers in plant breeding. Genomic locations of numerous genes or quantitative trait loci (QTLs) associated with agronomically important traits have been determined in several crop plants using linkage or association mapping approaches. Plant breeders always look for an easy, rapid and reliable method of selection of desirable plants in breeding populations. Conventionally, desirable plants are selected based on phenotypic observations. The phenotypic selection for complex agronomic traits is difficult, unpredictable and challenging. Once the marker-trait association is correctly established, the gene- or QTL-linked markers can be used to select plants carrying desirable traits, the process called marker-assisted selection (MAS). Marker-assisted backcrossing (MABC) has been widely used for transferring single major gene or combination of major genes into the background of elite cultivar; the process refers to gene pyramiding. Marker-assisted recurrent selection (MARS) and genome-wide association analysis (GWA) are considered potential MAS strategies for improvement of complex traits but still remain as theoretical possibilities in plant breeding. Though molecular markers and MAS have promises for improved plant breeding process, the marker-trait associations or QTLs are statistical associations, which are influenced by several factors such as trait heritability, phenotyping methods, marker density, population type and other experimental conditions that might lead to false positives. Therefore, a cautiously optimistic approach is necessary to consider MAS in crop breeding programmes. In this chapter, the potentials of genetic markers in plant breeding are described.