Fall 2014 HORT6033 Molecular Plant Breeding Instructor: Ainong Shi HORT6033 web site: http://comp.uark.edu/~ashi/MB

Molecular Plant Breeding Fall 2014 HORT6033 Molecular Plant Breeding Lecture 5 (09/08/2014) Genetic Diversity Example Homework Questions

Genetic 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. www.ask.com

Genetic Diversity in Breeding Select parents for crossing Breeding varieties to fit environments, stress, and consumer demand Genetic structure study and trait association analysis

Causes of Genetic Diversity Gene recommendation Gene mutation Gene transfer Selection Classification: INTERNAL USE ONLY

Genetic Diversity Genetic 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 small Fruit color: red vs yellow Tomato spotted wilt virus (TSWV): Resistance vs susceptible plant Resistant plant TSWV resistance: Resistance vs susceptible gene Sw-5 vs sw-5 Susceptible plant DNA sequence diversity SNP variation AY007366-sw5b TAATTTTCTCCTCAACATGTCGGCAAGAACATCAACCGTAGCTCCATTGTCGTCGGAACCTGTAACTTGACTGAAAATATCTTGTAATAACTCTCTCCGA 400 LA3667 ------------------------------A----------------------Y-R----------------G---------------------M--C-R 400 NY07-464 ------------------------------G----------------------T-A----------------A------------------------T-- 400 LA2823 ------------------------------G----------------------T-A----------------A------------------------T-- 400

Genetic Diversity in World-wide Spinach DNA extraction Genotyping by Sequencing SNP Discovery Spinach germplasm Data Analysis Plant 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 BGI SNP 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

Genetic 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.

The above cluster mainly consists of the spinach germplasm from Afghanistan, Iran, China, and India, Iran, and Japan

The above cluster mainly consists of the spinach germplasm from Turkey, indicating these turkey germplasm has the similarity genetic background.

Spinach Lines Developed by UAF All UAF spinach lines merged together, indicating The Good: UAF has special spinach germplasm; and The Bad: UAF spinach lines have narrow genetic background. Challenge: Continuously develop unique UAF spinach varieties Introgress other spinach genetic background into UAF spinach lines in order to broad genetic diversity

A SNP Set for Spinach Cultivar Identification So far, a SNP set consists of 15 SNPs postulated from genetic diversity analysis, which can distinguish and determine all 413 tested spinach genotypes. (left: 15 SNPs; right: example of spinach using the 15 SNPs) SNP_ID SNP short read record_298338 CAGCAAAAATGAAACCAAGTTTAAGAAATACCCA[A/T]AGTTCTATATTTGAAGAAGAGAAATTTCATAAGATACCTCTTGTATA record_298339 CAGCCCCATTCTAGAAATATTCATCCTCTACATCTTTAAAGGATGCCT[A/G]TTCACATCTCCATTCTTATAGTATCCACTTCTG record_298326 CAGCTTTTAAATCAGCTGAATTTCAACATTCGTAATCTGTTTGT[G/T]TATTATGTTTAAAGTTGTTTCTACTGATTATTGATGT record_349043 CAGCCTAAATCAAGTGGTRATGCATTTTCTCCCCT[C/T]TTCTGATTCACTTGAGGAATCTGTTTAGACATAGCTAATTTCATAA record_349021 CAGCAATTCATTGTTATTTAAGGTATCGTTAAGTGTATTCAACGATTTTTMTAACAAAATAACAAC[A/G]TTAAGGTTCGAGGAT record_349037 CAGCCTTATTAGGCAAACAAGTC[C/T]CTAGAACAAGATCAATTTGATGTTMAATTCCACGAATAGGAGGCGAACCTGGTGGTAA record_349001 CAGCTAAAAGATTGGAGTAATAGTCGAATCCTCGAACCTTAA[C/T]GTTGTTATTTTGTTAGAAAAATCKTTGAATACACTTAAC record_298342 CAGCTCAAATATTAAACCCTTGCTGTTGGGATCTACTGTACTGAAGTAGTAACTCTTCTAAGTAAAAGAATAAGCG[A/G]CTCTA record_298310 CAGCTGTGAA[A/G]CTGAAATTAGTGTCATTTGATGTTATTGTGTTATTGTGTTAATTTTCAAGTGTTGCCATTAATCAGTTTAC record_298366 CAGCTCAGCAAAATCTAGCAAAGTGAATGATTTGGATCAGACTTATGATTTTGTAA[A/T]GGGGGACCTTTTTCCCATACATTCC record_349055 CAGCTGGACCTRGGAAGGGGAACATGCATGTTATCTTTCTAGATGT[C/G]TTAAAAGTTAAAACAGGTGTGTTAAGCTTACTAAT record_298345 CAGCAATGGACATGAAGCAGGTCGAAAGACCCACTTTACTTT[A/C]GCTACAACACGAATATTACCACAATCGAAATTGCGRTTT record_298358 CAGCATCAGAATCTGTTTATTTCAGTCTAGATAATGTATATCAGCTTATTGCTAGGAACT[C/T]TGATCCCTCAAAGTTCACAAT record_349050 CAGCAGTCACAGCAACCTTTATGTCCCTGGGATGGAACTGACCGCGATTATCTGTAT[A/G]AAGAGGTRAGCTGTTTTGATCATC record_298400 CAGCCACTAGGGCAAGAGCAGAAACT[A/C]CTTGTCCAATACATACATTTTTAATATATAACCATGGTTATTTCATCTTTAGGGG

Tools for Genetic Diversity Analysis 1. Clustal X2 and TreeView X Clustal X2: http://www.clustal.org/ TreeView X: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html 2. MEGA 6 http://www.megasoftware.net/megacc.php

Examples for Sw-5 of Tomato Distance Stevens-Sw5b LA3667_Sw5ab LA3433_sw5 LA2823_sw5 NY07-464_sw5 Stevens-Sw5a   0.000 0.006 0.005 0.002 0.008 Sw-5 sample data to download

Examples for Spinach Genetic diversity in world wide spinach germplasm Fifteen SNP data for spinach variety determination Download the 15 SNP set data Genetic diversity in world wide spinach germplasm Download the 760 SNP data for ww spinach

Homework Use 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