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(1)

13th Annual

Solanaceae Conference

SolGenomics: From Advances to Applications

CONFERENCE

PROGRAM

September 12 — 16, 2016

Davis, California USA

(2)

Solanaceae Conference 2016 • UC Davis | SolGenomics2016.ucdavis.edu

1

S

CIENTIFIC

C

OMMITTEE

Siobhan Brady

, UC Davis

James Giovannoni

, USDA/BTI/Cornell

Glenn Bryan

, The James Hutton Institute

Antonio Granell

, Consejo Superior de Investigaciones Cientificas

Anne Britt

, UC Davis

Phyllis Himmel

, UC Davis

Roger Chetelat

, UC Davis

Jeanne Jacobs

, Plant & Food Research, New Zealand

Gitta Coaker

, UC Davis

Julin Maloof

, UC Davis

Luca Comai

, UC Davis

Cathie Martin

,

John Innes Centre

Ellen Dean

, UC Davis

Rich Ozminkowski

, Heinz

Massimo Delledonne

, Univ of Verona

Ann Powell

, UC Davis

Allen Van Deynze

, UC Davis

Neelima Sinha

, UC Davis

L

OCAL

O

RGANIZING

C

OMMITTEE

UC Davis, USA

Susan DiTomaso

Phyllis Himmel

Rebeca Madrigal

Ann Powell

Amanda Saichaie

Julie Tillman

Allen Van Deynze

G

ENERAL

C

ONFERENCE

I

NFORMATION

• Conference Center building will open daily at 7:30 am.

• Conference Center restrooms are located adjacent to the registration desk; Additional restrooms

are available on the second floor.

• Meal and drink tickets are placed in the plastic sleeve of the name badges.

• Drink tickets are needed for beer and wine at all evening social events. Non-alcoholic drinks and

water available at no cost. Additional beer and wine drinks may be purchased (cash only, USD).

• All conference abstracts available at

SolGenomics2016.ucdavis.edu/program

• Platinum and Gold level sponsor representatives are encouraged to be present at their company

hosted lunch tables.

• Emergency help is available by dialing 911 from a land line or (530) 752-1230 from a mobile

phone. Do not dial 911 from a mobile phone. For additional campus emergency and safety

information, visit www.ucdavis.edu/emergency/. For status or information during an emergency,

call the campus Emergency Status Line at (530) 752-4000.

• In case of emergency, conference attendees should gather on VanderHoef Quad.

C

ONFERENCE

P

OLICIES

• Name badges should be worn at all Conference functions.

• For all evening social events, guests may not leave event area with alcohol in hand.

• Lunch, reception and banquet tickets must be turned in at each meal.

• Cell phones should be turned off during all scientific sessions.

• Photos are discouraged during talks.

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S

ESSION

C

HAIRPERSONS

Session I • DIVERSITY-TAXONOMY/CROP GERMPLASM DIVERSITY

Ellen Dean, UC Davis • Irma Ortiz, UC Riverside

Session II • BARRIERS TO BREEDING

Roger Chetelat, UC Davis • Benny Julissa Ordonez Aquinno, UC Davis

Session III • GENOMES & GENOME TECHNOLOGIES

Massimo Delledonne, Univ. of Verona • Arsenio Ndeve, UC Riverside

Session IV • HIGH-THROUGHPUT PHENOTYPING

Allen Van Deynze, UC Davis • Lav Yadav, West Virginia State Univ.

Session V • GENE-EDITING AND NEW BREEDING TECHNOLOGIES

Anne Britt, UC Davis • Julie Pedraza, California State Univ., Fresno

Session VI • EPIGENOMICS AND METHYLATION

Luca Comai, UC Davis • Brittany Davenport, West Virginia State Univ.

Session VII • GENOMICS-ASSISTED BREEDING

Jeanne Jacobs, Plant & Food Res NZ • Kieu Nga Tran, Louisiana State Univ.

Session VIII • SYSTEMS BIOLOGY AND NETWORKS

Siobhan Brady, UC Davis • Sophia Jinata, UC Davis

Session IX • ABIOTIC STRESSES

Julin Maloof, UC Davis • Lumariz Hernandez-Rosario, Univ. of Puerto Rico

Session X • RESISTANCE, PATHOGENS, PESTS AND MICROBIOMES

Gitta Coaker, UC Davis • Kevin Babilonia, Texas A&M

Session XI • TUBERS AND ROOT SYSTEMS

Glenn Bryan, The James Hutton Institute • Justin Medina, Cal Poly Pomona

Session XII • FLOWERS, SEEDS AND FRUIT

James Giovannoni, USDA/BTI/Cornell • Kimberly Rodriguez, New Mexico State Univ.

Session XIII • PLANT DEVELOPMENT AND REGULATION

Neelima Sinha, UC Davis • Timothy Batz, Calif. State Polytechnic Univ., Pomona

Session XIV • METABOLITES, FLAVOR AND QUALITY

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Solanaceae Conference 2016 • UC Davis | SolGenomics2016.ucdavis.edu

101

Haploid induction can be used to rapidly introduce novel genetic combinations into crop varieties. We

have previously demonstrated that haploid induction via uniparental genome elimination in

Arabidopsis is able to create a range of novel karyotypes such as truncations, deletions,

rearrangements, or minichromosomes derived from the haploid inducer genome. In the potato haploid

induction system, residual fragments of Solanum tuberosum Group Phureja haploid inducer genome

have been reported in haploid progeny, but these introgression events have not been characterized

with genome sequencing approaches. Therefore, we plan to explore the extent of dosage variation

produced by potato haploid induction crosses using whole-genome sequencing. We will test the

hypothesis that some of the haploid progeny from the haploid inducing cross in potato will exhibit

novel genome dosage variation, or may contain DNA fragments from the haploid inducer genome.

Here, we report a pilot-scale chromosome dosage analysis of F1 haploids (n=6) produced from a S.

tuberosum Group Andigena × S. tuberosum Group Phureja haploid induction cross. We found that one

of the six analyzed lines exhibited a truncated chromosome 4, which suggests that chromosome

remodeling can occur during in vivo haploid induction in potato. In order to characterize a broader

range of chromosome dosage variation, including potential introgressions from the Phureja haploid

inducer, we plan to generate and sequence 400 additional putative haploid lines.

308-TH.

GENOME WIDE ASSOCIATION STUDIES CORRECTING POPULATION STRATIFICATION IN

PEPPER CORE COLLECTION

Lee H-Y.

1

, Han K.

1

, Hur O-S.

2

, Go H-C.

2

, Kwon J-K.

1

, Sung J-S.

2

, Kang B-C.

1

1

Department of Plant Science and Vegetable Breeding Research Center CALS, Seoul National

University, Seoul 151-921, Korea;

2

National Academy of Agricultural Science, Rural Development

Administration, Jeonju 560-500, Korea

Contact: Tel: +82-2-880-4563, E-mail: bk54@snu.ac.kr

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 performing 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, a 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. MLM using Q

values combined with kinship matrix estimated from stratification methods were used to identify

quantitative trait loci controlling the variation of ten agronomic traits. These results will help to

understand associations between phenotype and genotype and also will be used for validation of the

candidate genes or quantitative trait loci previously identified in pepper.

309-TH.

IDENTIFYING NOVEL SMALL PEPTIDES IN TOMATO USING RIBOSOME PROFILING

Hsu P.Y.

1

, Calviello L.

2

, Wu H.L.

3

, Li F.W.

1,4

, Rothfels C.

4

, Ohler U.

2

, Benfey P.N.

1,5

1

Duke University, Durham, NC, USA;

2

Max Delbrück Center, Berlin, Germany;

3

North Carolina State

University, Raleigh, NC, USA;

4

University of California, Berkeley, Berkeley, CA, USA;

5

Howard Hughes

Medical Institute, Durham, NC, USA

Contact: Polly Hsu,

polly.hsu@duke.edu

Small peptides play important roles in short and long distance signaling in plants. They regulate plant

growth and development, interactions between plants and the environment, as well as interactions

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Hea-Young Lee

1

, Koeun Han

1

, On-Sook Hur

2

, Ho-Cheol Go

2

, Jin-Kyung Kwon

1

, Jung-Sook Sung

2

and Byoung-Cheorl Kang

1*

1Department of Plant Science and Vegetable Breeding Research Center CALS, Seoul National University, Seoul 151-921, Korea; 2National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea. *Corresponding author Byoung-Cheorl Kang bk54@snu.ac.kr+82-2-880-4563

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 performing 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. As a result, MLM using Q values combined with k-medoids clustering estimated from stratification methods were used to identify quantitative trait loci controlling the variation of ten agronomic traits. These results will help to understand associations between phenotype and genotype and also use for validate the candidate genes or quantitative trait loci previously identified in pepper.

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

Detection of candidate QTLs associated with interested phenotypes

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

ACKNOWLEDGEMENT

Genomic structure of pepper GWAS population

Figure 4. Population structure of the Capsicum core collection (CC250) using GBS data. ∆K 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 4).

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 351 Capsicum GWAS population using PstI-MseI double digest enzyme set (average SNP depth: 86). 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 (Figure 3).

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

•PstI and MseI 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 ∆K Whole population Sub population 1 Sub population 2

Figure 3. SNP distribution among 12 pepper chromosomes. Over 33,843 SNPs were used for construct

the high density haplotype map.

Using MLM (K+Q), a total of 56 candidate QTLs associated with 12 various agronomic traits was detected among 12 Capsicum chromosome.

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. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using

multilocus genotype data. Genetics. 2000;155(2):945–59.

4. Han K, Jeong H-J, Yang H-B, Kang S-M, Kwon J-K, Kim S, et al. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum). DNA Res. 2016;23(2):81–91.

GWAS on Capsicum GWAS population of various interested agronomic 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) Plant height, (B) Plant width, (C)

CHR 1 CHR 12 CHR 2 CHR 3 CHR 4 CHR 5 CHR 6 CHR 7 CHR 8 CHR 9 CHR 10 CHR 11

Detected SNP positions among each chromosome based on

Capsicum reference genome (C. annuum cv. CM334)

SNPs distribution among each chromosome Accessions of G W AS populat ion Number of SNPs 2,540 3,433 2,828 3,934 2,428 2,745 3,296 2,504 1,762 2,640 2,654 3,079

(A) Plant height (B) Plant width (C) Number of branch (D) Stem thickness

* INL-1 (Han, 2016)

* FL-3.1 (Han, 2016)

(E) Node length (F) Fruit length (G) Fruit width (H) Fruit weight

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