1. Fall 2014 HORT6033 Molecular Plant Breeding
Instructor: Ainong Shi
HORT6033 web site:

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

3. 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.

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

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

6. 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
AY sw5b TAATTTTCTCCTCAACATGTCGGCAAGAACATCAACCGTAGCTCCATTGTCGTCGGAACCTGTAACTTGACTGAAAATATCTTGTAATAACTCTCTCCGA
LA A Y-R G M--C-R
NY G T-A A T
LA G T-A A T

7. 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

8. 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.

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

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

11. 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

12. 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

13. Tools for Genetic Diversity Analysis
1. Clustal X2 and TreeView X
Clustal X2:
TreeView X:
2. MEGA 6

14. 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

15. 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

16. 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