i
Program
2016 한국육종학회-차세대BG21사업단-GSP사업단 공동심포지엄
Gene, Genome & New Technology for Plant Breeding
2016년 6월 29일(수) ~ 7월 1일(금), 라마다플라자 청주호텔
1일째 [2016. 6. 29. 수]
19:00~ 이사회의 및 조직위원회의
2일째 [2016. 6. 30. 목]
09:00~09:50 공동심포지엄 학술발표회 등록 및 포스터 부착
09:50~10:00
개회식
개회사
- 정영수 교수 (조직위원장, 동아대학교)
환영사
- 조용구 교수 (회장, 충북대학교)
<< 1부 Plenary Session >>
- 좌장 : 고희종 교수 (서울대학교)
10:00~10:40
▸Doubled Haploid (DH) technology in maize breeding: Application and technology for
production of DH lines
- Dr. Chaikam, CIMMYT, Mexico
10:40~11:20 ▸Finding mineral element transporters for better and safe production of rice
- Dr. Jian Feng Ma, Okayama University, Kurashiki, Japan
11:20~12:00 ▸Function of Fibrillin protein in photosynthetic metabolism
- 김현욱 교수 (세종대학교)
12:00~13:20 점심시간
- 좌장 : 오대근 교수 (한국농수산대학)
13:20~14:00 ▸Revisiting domestication to revitalize crop improvement: the florigen revolution
- Dr. Zach Lippman, Cold Spring Harbor Laboratory, USA
14:00~14:40 ▸Manipulating Fruit and Vegetable Quality Traits
- Dr. David Brummell, Plant & Food Research, New Zealand
14:40~15:20 ▸Designing Crops for Global Food Security:Digitizing Plant Phenotypes
- Dr. Maurice Moloney, Global Institute for Food Security, Canada
15:20~15:40 휴식
2일째 [2016. 6. 30. 목]
<< 2부 한국육종학회 분과발표 & 포스터 발표 >>
15:40~17:40
▸분과발표 OA 수량 및 저항성육종
- 좌장 : 김용호 교수 (순천향대학교), 조영찬 박사 (국립식량과학원)
▸분과발표 OB 품질육종 및 유전변이
- 좌장 : 김보경 과장 (국립식량과학원) 강성택 교수 (단국대학교)
▸분과발표 OC 분자육종 및 유전공학
- 좌장 : 강권규 교수 (한경대학교), 박용진 교수 (공주대학교)
17:40~18:00 한국육종학회 정기총회
18:00~18:20 포스터 발표
18:20~ 특별공연 및 간친회
3일째 [2016. 7. 1. 금]
<< 3부 Concurrent Session >>
주요 작물에서 유전체 정보활용 육종가 친화형 인터페이스 연구 소개 (농생물게놈활용연구사업단)
- 좌장 : 유의수 박사 ((주)파이젠)
09:00~09:25 ▸가지과 유전체 활용을 위한 생물정보분석 파이프라인 및 데이터베이스 TGsol 현황
- 조성환 박사 ((주)씨더스)
09:25~09:50 ▸두과작물 유전체정보 기반 분자육종 활용을 위한 플랫폼 개발
- 최홍규 교수 (동아대학교)
09:50~10:15 ▸콩 유전체 육종 지원용 Korean Soya Base 소개
- 김남신 박사 (한국생명공학연구원)
10:15~10:40
▸벼 유전체육종 연구의 진전 및 소규모 연구실간의 Resource 공유체계 구축 : 재료 정보 프로그램
연구경험 공유
- 박용진 교수 (공주대학교)
Genome editing and molecular farming (GM작물개발사업단 & 식물분자육종사업단)
- 좌장 : 조현석 박사 (국립농업과학원 생물안전성과)
09:00~10:40
▸Versatile application of CRSPR/Cas9 system in plant research
- 배상수 교수 (한양대학교)
▸Transgenic plants producing green-vaccine for CSFV(classical swine fever virus) lead on
plant biotechnology-based product on market
- 손은주 박사 ((주)바이오앱)
10:40~11:00 휴식
iii
3일째 [2016. 7. 1. 금]
<< 3부 Concurrent Session >>
- GSP 채소종자사업단 & GSP 원예종자사업단
▸좌장 : 임용표 단장 (채소종자사업단)
09:00~10:40
▸육성가 권리보호와 종자산업의 발달
- 이승인 박사 (국립종자원)
▸종자검정서비스 확대를 위한 국립종자원의 전략
- 소은희 박사 (국립종자원)
▸좌장 : 노일섭 단장 (원예종자사업단)
▸Breeding for Pyramiding Target-genes and Selection of F1 Hybrids by Marker Assisted
Selection in Tomato
- 김명권 박사 (토마토생명공학연구소)
▸Gene Identification, Expression Analysis and Breeding for Enhanced Glucosinolate Biosynthesis
in Brassica
- Dr. Arif Hasan Khan Robin (Sunchon National University)
GSP 식량종자사업단
-▸좌장 : 조영찬 박사 (국립식량과학원)
09:00~10:40
▸Specialty corn breeding at Sweet Seeds in Thailand to the tropical world
- Dr. Taweesak Pulam (Sweet Seeds. Inc.)
▸중국의 벼 육종기술 및 육종 현황
- Dr. Han Longzhi (Institute of Crop Sciences of Chinese Academy of Agricultural Sciences)
▸Application of Biotechnology in Developing New Rice Varieties For High Temperature
Tolerance in the Philippines
- Dr. Norvie Manigbas (PhilRice)
▸Rice production and the change of major diseases during the period of climate change in
Vietnam
- Dr. Dung Laitien (Plant Protection Research Institute, Vietnam)
10:40~11:00 휴식
<< 4부 Plenary Session >>
▸좌장 : 서용원 교수 (고려대학교)
11:00~11:40 ▸CRISPR RNA-guided Genome Editing in Human Stem Cells, Animals, and Plants
- 김진수 교수 (서울대학교)
11:40~12:20 ▸CRISPR Genome Editing in Outcrossing Woody Perennials
- Dr. CJ Tsai, University of Georgia, USA
PC-53 Characterization of Cytochrome P450 (CYP) Genes Related to Saponin Biosynthesis
in
Platycodon grandiflorum
214
Sohyeon Park, Jemin Yoo, Yurry Um, Ok Tae Kim, Chang Pyo Hong, Seong-Cheol Kim, Yi Lee
PC-54 Analysis of Genetic Diversity in 5
Codonopsis
Species Based on SSR Markers 215
Sohyeon Park, Serim Kim, Jinsu Gil, Yurry Um, Hee Chung, Ok Tae Kim, Ho Bang Kim,
Seong-Cheol Kim, Yi Lee
PC-55 The CRISPR/Cas9-mediated Genome Editing in Banana Cells 216
Youjin Shin, Jin-Soo Kim, Jae-Young Yun
PC-56 Development of Chloroplast InDel Markers to Distinguish
Angelica
Species 217
Sohyeon Park, Sangik Park, Jinsu Gil, Yurry Um, Hee Chung, Seong-Cheol Kim, Yi Lee
PC-57 High-throughput transcriptome analysis for identifying genes determining flowering time 217
Cheol-Won Lee, Yong Weon Seo
PC-58 Candidate Gene Analysis for the Genes Controlling the Yellow Color in
Capsicum annuum
Cultivar Micropep 218
Ayoung Jung, Juhun Lee, Jin-Kyung Kwon, Suna Kim, Byoung-Cheorl Kang
PC-59 Identification of New Resistance Sources for
Cucumber mosaic
virus
New Isolate-P1 (CMV-P1)
in the Germplasm Collection of Capsicum spp. 219
Seula Choi, Myeong-Sook Han, Jin-Kwan Jo, Joung-Ho Lee, Eun-Ho Son, Byoung-Cheorl Kang
PC-60 Genetic Mapping of Resistance Sources Against ChiVMV (
Chili veinal mottle virus
) in Hot Pepper 220
Joung-Ho Lee, Jeong-Tak An, Koeun Han, Seula Choi, Muhammad Irfan Siddique, Byoung-Cheorl Kang
PC-61 Correcting Population Stratification in Pepper Core Collection for Genome-wide Association
Studies (GWAS) 221
Hea-Young Lee, Koeun Han, Jin-Kyung Kwon, Byoung-Cheorl Kang
PC-62 Hormone Related Transcriptome Analysis of Wheat During Pre-harvest Sprouting
and Exogenous ABA Treatment 222
Yong Jin Lee, Jae Yoon Kim, Yong Weon Seo
PC-63 Probing High-yield Traits of Soybean by Transforming Senescence-delay Genes 223
Hyun Suk Cho, Jin Ho Yang, Jin Sol Park, Hye Jeong Kim, Yoon Jeong Lee, Jae Seong Kim,
Hyun Hee Im, Ki Jung Lee, Dong Hee Lee, Young Soo Chung
221
PC-61 ◆1
Correcting Population Stratification in Pepper Core Collection for Genome-wide Association
Studies (GWAS)
Hea-Young Lee*, Koeun Han, Jin-Kyung Kwon, Byoung-Cheorl Kang*
Department of Plant Science and Vegetable Breeding Research Center CALS, Seoul National University, Seoul 151-921,
Korea
Genome-wide association study (GWAS) is an effective approach for identifying genetic variants associated to useful
agronomic traits. GWAS has emerged as a powerful approach for identifying genes underlying complex diseases or
morphological traits at an unprecedented rate. In such studies, it is very important to correct for population stratification,
which refers to allele frequency differences between cases and controls due to systematic ancestry differences. Population
stratification can cause false positive findings if not adjusted properly. As we are planning to perform GWAS for various
agronomic traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker
coverage (>19,000 SNPs) for a 250 pepper core collection. Using GBS platform, high density haplotype map was
constructed and various stratification methods, including distance based phylogenetic methods, principal component analysis
(PCA), and bayesian phylogenetic methods (STRUCTURE) were performed to show the genetic diversity and population
stratification. These results will not only find genetic variants among pepper accessions but also provide powerful evidence
for reducing first positive error to perform GWAS in large scale studies.
Hea-Young Lee
1
, Koeun Han
1
, Jin-Kyung Kwon
1
, and Byoung-Cheorl Kang
1*
1
Department of Plant Science and Vegetable Breeding Research Center CALS, Seoul National University, Seoul 151-921, Korea,
*Corresponding author Byoung-Cheorl Kang
bk54@snu.ac.kr
+82-2-880-4563
Correcting population stratification in pepper core collection for
genome-wide association studies (GWAS)
Genome-wide association study (GWAS) is an effective approach for identifying genetic variants associated to useful agronomic traits. GWAS has emerged as a powerful approach for
identifying genes underlying complex diseases or morphological traits at an unprecedented rate. In such studies, it is very important to correct for population stratification, which
refers to allele frequency differences between cases and controls due to systematic ancestry differences. Population stratification can cause false positive findings if not adjusted
properly. As we are planning to perform GWAS for various agronomic traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker
coverage (>33,000 SNPs) for a 250 pepper core collection. Using GBS platform, high density haplotype map was constructed and various stratification methods, including distance
based phylogenetic methods, principal component analysis (PCA), and bayesian phylogenetic methods (STRUCTURE) were performed to show the genetic diversity and population
stratification. These results will not only find genetic variants among pepper accessions but also provide powerful evidence for reducing first positive error to perform GWAS in large
scale studies.
ABSTRACT
OBJECTIVES
MATERIALS & METHODS
Detection of genome-wide SNPs among pepper GWAS population using
genotyping-by-sequencing (GBS) approach
Construction of high density haplotype map
Population structure analysis using various stratification methods
A pepper GWAS population including 9 species, consisting of 351 accessions
was constructed by combining three different collections.
Capsicum
species
included in this population are shown in figure 1.
RESULTS
This work was carried out with the support of "Cooperative Research Program
for Agriculture Science & Technology Development (Project No.
PJ011204012016)" Rural Development Administration, Republic of Korea
ACKNOWLEDGEMENT
Genomic structure of pepper GWAS population
Figure 3. Population structure of the
Capsicum
core collection (CC250) using GBS data. ΔK
reached its maximum value when K=2 following the
ed-hoc
method. Subpopulations were
grouping by Q. Each subpopulation was separated in to two subgroups.
REFERENCE
SNP observation in high density haplotype map
Based on the Bayesian phylogenetic methods, whole population showed two subpopulations
as
C. annuum
and the other species. The first subpopulation which contains the other species
was also divided in two subgroups as
C. baccatum
and the other species. The second
subpopulation which contains all the
C. annuum
was tend to separate by fruit shape as hot
pepper type and bell pepper type (Figure 3).
Distribution of pepper GWAS population
Plant material
Genotyping-by-sequencing (GBS)
To better understand the genetic diversity of germplasm, phylogenetic analysis
and PCA were performed by DARwin 6.0.9 (Perrier and Jacquemoud-Collet, 2006).
Population structure was identified using STRUCUTRE 2.3.4 software.
Overall 3,000,000 SNPs were detected among pepper GWAS population. SNPs with > 50%
missing data and monomorphic SNPs were dropped from the data set. After strong SNP
filtering, 33,843 SNPs were remained with call rates > 0.5.
SNP observation and haplotype map construction
Population structure and genetic diversity analysis
Pepper GWAS population
Pepper core collection (250)
Accessions with additional
useful traits (51)
ChiVMV
CMV
PepMoV
TMV
Anthracnose
Powdery
Mildew
Core collection in other
Capsicum species (50)
C. annuum
226
C. baccatum
47
C. chacoense
2
C. chinense
46
C. frutescens
25
C. eximium
2
C. galapagoense
1
C. praetermissum
1
C. pubescens
1
Total
351
Figure 1. Pepper GWAS population using in this study. A total of 351 accessions were
placed in this population constructed by combining three different pepper
collections.
DNA of germplasm was extracted by CTAB method. Two restriction enzymes
(
PstI-MseI
), and a compatible set of 96 barcode were used to prepare the GBS
library. Single end sequencing was performed on four lanes of an Illumina HiSeq
2000 at the Macrogen Inc (Seoul, Korea).
The CLC Genomics Workbench was used to check sequencing quality (QC) and
trim the sequence reads. Two software tools, BWA and GATK were used for the
processing of Illumina sequence read trimmed data. Haplotype map was
constructed using FILLIN in TASSEL 5 (Figure 2).
SNP calling
CLC Genomics Workbench
•Quality trimming and demultiplexing using barcode
BWA
•BWA-MEM (0.7.12)
GATK
•GATK Unified Genotyper
•Filtering SNPs with QUAL >= 30, and minimum depth 3
Library construction &
Sequencing
GBS library
•
Pst
I and
Mse
I double digestion
HiSeq 2000
•Run mode: 101 single end
Imputation
TASSEL FILLIN
•Construction of haplotype map
•Imputation of missing SNPs by haplotype map
High-quality SNPs
Figure 2. Workflow of SNP calling and haplotype map construction.
K=2
Other species
C. annuum
C. baccatum
C. chinense
C. frutescens
Hot pepper type
Bell pepper type
K=2
K=2
0
2000
4000
6000
8000
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
0
500
1000
1 2 3 4 5 6 7 8 9 10 11 12
0
500
1000
1500
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
K
ΔK
Whole population
Sub population 1
Sub population 2
C. frutescens
+
1
C. eximium
(Group 2)
C. chinense
+
1
C. praetermissum
(Group 3)
C. annuum
(Group 4)
C. annuum
(Group 5)
C. annuum
(Group 6)
C. annuum
(Group 7)
C. annuum
(Group 8)
Figure 4. Genetic relatedness among the core collection assessed by PCA (A) and neighboring
joining method (B) after haplotype imputation. Eight groups (Group 1-8) were distinguished
by distance between branches; group 1 included
C. baccatum
;
group 2 included
C. frutescens
with 1
C. eximium
;
group 3 included
C. chinense
with 1
C. praetermissum
;
most of
C. annuum
species spread among group 4 to 8; group 5 and 6 consist of hot pepper type; group 7 and 8
consist of bell pepper type.
Axis 1: 47.26%
A
xi
s
2:
27
%
C. baccatum
C. chinense
C. frutescens
C. annuum
To understand the population stratification in pepper GWAS population, whole accessions
were plotted in distance metrics. The first and second axes explained 47.26% and 27% of the
genotypic variance, respectively, that clearly separated
C. annuum
from
C. baccatum
and the
other species. In right below of matric,
C. frutescens
and
C. chinense
showed admixture slightly.
Overall, PCA analysis showed that four distinct sub population was existent in GWAS
population (Figure 4A). For an unrooted phylogenetic tree, eight groups were figure out
among the whole accessions. And the distribution of clusters showed similar patterns of PCA
results that groups were divided in species level (Figure 4B).
(A)
(B)
1. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A
robust, simple genotyping-by-sequencing (GBS) approach for high diversity
species. PLoS One. 2011;6(5):1–10.
2. Liu L, Zhang D, Liu H, Arendt C. Robust methods for population stratification
in genome wide association studies. BMC Bioinformatics. 2013;14(1):132.
3. Perrier X, Jacquemoud-Collet, JP. 2006. DARwin software
4. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using
multilocus genotype data. Genetics. 2000;155(2):945–59.
GWAS of various fruit traits
Figure 5. Manhattan plots of association p-values over the 12 pepper chromosome. MLM (K+Q)
model was used to screen for association between genotype and (A) Fruit length, (B) Fruit
width, (C) Fruit weight, and (D) Pericarp thickness.