3Genetic Diversity and Benefit Genetic diversity refers to any variation in the nucleotides, genes, chromosomes, or whole genomes of organisms. It entails looking at the genetic characteristics in the genetic makeup of a species. It is different from genetic variability, which describes the tendency of genetic characteristics to vary.Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment.
4Genetic Diversity in Breeding Select parents for crossingBreeding varieties to fit environments, stress, and consumer demandGenetic structure study and trait association analysis
5Causes of Genetic Diversity Gene recommendationGene mutationGene transferSelectionClassification: INTERNAL USE ONLY
6Genetic DiversityGenetic variation between and within species, which is measured by determining the proportion of polymorphic loci across the genome, or by the number of heterozygous individuals in a population.Fruit size: large vs smallFruit color: red vs yellowTomato spotted wilt virus (TSWV):Resistance vs susceptible plantResistant plantTSWV resistance:Resistance vs susceptible geneSw-5 vs sw-5Susceptible plantDNA sequence diversitySNP variationAY sw5b TAATTTTCTCCTCAACATGTCGGCAAGAACATCAACCGTAGCTCCATTGTCGTCGGAACCTGTAACTTGACTGAAAATATCTTGTAATAACTCTCTCCGALA A Y-R G M--C-RNY G T-A A TLA G T-A A T
7Genetic Diversity in World-wide Spinach DNA extractionGenotyping by SequencingSNP DiscoverySpinach germplasmData AnalysisPlant materials: A total of 413 spinach genotypes were used in this study, including 323 USDA-GRIN germplasm originally collected from 33 countries.DNA extraction: genomic DNA is extracted from spinach leaves using the CTAB.Sequencing: using GBS by HiSeq 2000 in BGISNP discovery: GBS data analysis using DNASTAR Lasergene Genomics Suite, TASSEL; Around half million SNPs were discovered from the 413 spinach genotypes using GBS by de novo assembly.Genetic Diversity
8Genetic Diversity in Spinach 380 SNPs were used for genetic diversity analysis. The genetic diversity analysis indicated that there was a geography (country) factor during spinach variety development and spinach production.
9The above cluster mainly consists of the spinach germplasm from Afghanistan, Iran, China, and India, Iran, and Japan
10The above cluster mainly consists of the spinach germplasm from Turkey, indicating these turkey germplasm has the similarity genetic background.
11Spinach Lines Developed by UAF All UAF spinach lines merged together, indicatingThe Good: UAF has special spinach germplasm; andThe Bad: UAF spinach lines have narrow genetic background.Challenge:Continuously develop unique UAF spinach varietiesIntrogress other spinach genetic background into UAF spinach lines in order to broad genetic diversity
13Tools for Genetic Diversity Analysis 1. Clustal X2 and TreeView XClustal X2:TreeView X:2. MEGA 6
14Examples for Sw-5 of Tomato DistanceStevens-Sw5bLA3667_Sw5abLA3433_sw5LA2823_sw5NY07-464_sw5Stevens-Sw5a0.0000.0060.0050.0020.008Sw-5 sample data to download
15Examples for Spinach Genetic diversity in world wide spinach germplasm Fifteen SNP data for spinach variety determinationDownload the 15 SNP set dataGenetic diversity in world wide spinach germplasmDownload the 760 SNP data for ww spinach
16HomeworkUse Clustal X2 and TreeView X to do genetic diversity for 15 SNP data of spinach lines;Use MEGA 6 to do genetic diversity for 15 SNP data of spinach lines;Use MEGA 6 to do genetic diversity for world wide spinach germplasm