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. 2016 Nov 30;6:38081. doi: 10.1038/srep38081

Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L

Padma Nimmakayala 1,*, Venkata L Abburi 1,*, Thangasamy Saminathan 1, Suresh B Alaparthi 1, Aldo Almeida 1, Brittany Davenport 1, Marjan Nadimi 1, Joshua Davidson 1, Krittika Tonapi 1, Lav Yadav 1, Sridhar Malkaram 1, Gopinath Vajja 1, Gerald Hankins 1, Robert Harris 1, Minkyu Park 2, Doil Choi 2, John Stommel 3, Umesh K Reddy 1,a,*
PMCID: PMC5128918  PMID: 27901114

Abstract

Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.

The pepper genus Capsicum originated in Bolivia and consists of 25 to 30 species; five are domesticated: C. annuum, C. baccatum, C. chinense, C. frutescens, and C. pubescens1,2. C. annuum is the most popular and was first introduced from the West Indies to Europe in March 1493, with the first travels of Christopher Columbus3,4. Trade routes between Europe, Middle-East and Asia promoted additional introductions and reciprocal exchanges, so multiple introductions were rapidly cultivated in most tropical, Mediterranean and temperate regions of the world. In these secondary diversification centers, thousands of landraces have been selected for 4 to 5 centuries by growers to fit new environments and local consumption habits and trade, which has resulted in wide phenotypic diversity of pepper cultivars5,6,7.

For many crop species, identification and utilization of single nucleotide polymorphisms (SNPs) have become economical because of the availability and abundance of various high-throughput technologies. Recently, three whole-genome sequence (WGS) drafts of hot pepper were released for public use, which opened up unique opportunities for pepper research. The WGS for C. annuum cv. CM334 is 650.2 Gb (186.6× genome coverage)8. WGS for Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum) were made available by Qin et al.9. An examination of population structure, diversity at the molecular level, linkage disequilibrium (LD) distribution across various chromosomes and quantitative trait loci (QTL) estimated by model-based association mapping would provide insights into the evolution of various traits among C. annuum cultivars7. LD distribution information across the C. annuum genome will help group SNPs into haplotypes and, their use in genome analysis can lead to understanding the consequences of selection and breeding histories across the collections of C. annuum L.

Genome-wide association study (GWAS) with SNPs generated by genotyping by sequencing (GBS) has been widely used in all major crops including maize, rice, barley, tomato, wheat, sorghum, soybean, watermelon and several other important plant species10,11,12,13,14 and found effective for mining new genes; however, the population structure must be resolved accurately to reduce spurious associations because of confounding effects of subpopulations. The current research aims to identify genomic segments linked to various fruit traits and capsaicin accumulation in diverse collections of C. annuum. Despite several QTL studies of pepper15,16,17,18,19,20, the current study is unique in that it utilizes WGS drafts for anchoring SNPs and systematic GWAS pipelines to identify SNP markers for various fruit-related traits with special reference to capsaicinoid content and fruit weight (FW). It aims to identify genome-wide effects on capsaicinoid content and fruit weight (FW) in C. annuum populations by using SNPs identified by GBS.

Results

SNP development

A total of 250,493,661 reads were available for analysis after quality trimming and 56.0% of these were aligned to unique positions and 24% to multiple positions on the physical map. Accession-wise reads are presented in Table S2. A total of 66,960 SNPs were identified from the reads obtained for the 94 diverse C. annuum accessions studied; 7678, 7751, 8201, 6285, 4724, 6087, 5230, 3873, 3826, 4279, 3768 and 5268 SNPs were mapped to the WGS draft (Kim et al.8) and located on chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12, respectively. When screened for minor allele frequency (MAF) of 0.05% and call rate > 95%, total SNPs were reduced to 7,331 with 839, 683, 1007, 459, 566, 715, 464, 423, 479, 641, 543 and 512 on chromosomes 1 to 12, respectively. In addition, we identified 2,521 SNPs (containing MAF 0.05) located in various exons. SNPs in exons of various genes were 288, 295, 346, 131, 183, 231, 162, 153, 154, 218, 164 and 196 on chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12, respectively. We noted presence of one SNP at every 40.7 kb across the genome, with average gap size of 26.08 kb, and one SNP at every 78.8 kb in the coding regions. After excluding for MAF present at 0.05%, we noted one SNP at every 172.2 kb across the whole genome and one SNP every 386 kb in the exons. Heterozygosity (Table S3) ranged from 18% to 3% among various accessions. Sangria, Jyothi, Hungarian semi hot, Tormenta hot, Costeno Amarillo, Cayenne Purple, PI439355, Watermelon, Numex R Naky, Jalapeno pepper, Prik ki nu and Red Rocket were the most highly heterozygous, from 18% to 9%. Mean heterozygosity was 6%, so the accessions in the study were generally homozygous at most of the polymorphic loci and hence suitable for GWAS analysis. The mean MAF was 1892 (range 2711 [Tepin Guatemala] to 1115 [Pimento Sweet Apple]).

Population stratification and effect of capsaicin content and FW

We used PCA of the 7,331 SNPs to classify domesticated and wild C. annuum peppers. Two PCA figures based on capsaicin content (CA) and FW classifications were created to understand the relationships of accessions. This analysis produced a close cluster of hot peppers on CA-PCA and bell peppers as separate cluster (Fig. 1). Sangria, Bellingrath Gardens, Prik ki nu, Pepperoncini, Red Rocket, Hot Red Rocket, Jwala, PI 439355, Jyothi, Hinkelhatz pepper, PI 636424, De Arbol, Goat’s Weed, Costeno Amarillo, Cayenne Purple and Yellow Peter were clustered around the wild accessions. Similarly, three serrano peppers, namely Mexican serrano, Serrano pepper and Serrano Tampiqueno, were grouped together and distant from the rest of the accessions. PCA placement of the various accessions can be noted from the eigen values presented in Table S4. To validate the results of PCA, we used a model-based approach for population structure analysis to analyze the entire panel of 94 C. annuum accessions grouped by CA and FW (Fig. 2). Use of Structure Harvester provided Delta K values, which showed K-4 as the most appropriate.

Figure 1. Principal component analysis (PCA) showing distribution of global Capsicum annuum accession collections with 7, 331 single nucleotide polymorphisms (SNPs).

Figure 1

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(A) PCA with accessions grouped by capsaicin content. (B) PCA with accessions grouped by fruit weight. See Table S2 for a list of accessions and for respective eigen values to locate individual accessions on the graph.

Figure 2. Admixture in subpopulations resolved using 7, 331 single nucleotide polymorphisms (SNPs) along with capsaicin content (high, medium and low) (B) and SNPs and Fruit weight (large, medium and small) among C. annuum accession collections by population structure, a model-based approach.

Figure 2

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(A) K4 had the highest peak (based on Delta K distribution), so four clusters sufficiently define C. annuum population structure based on capsaicin content and fruit weight.

We examined allele sharing across the panel by calculating identity by state (IBS) coefficients among all pairs of accessions (Fig. 3). Allele sharing clearly tracks subpopulation ancestry as identified by PCA and Structure outputs. The mean observed IBS sharing was greatest for large-sized sweet peppers (0.97) as compared with small-sized hot peppers (0.85), with relatively little IBS sharing between high and low capsaicin-containing peppers (0.54 ± 0.94). The highest IBS sharing among high and low capsaicin content types was between Burning Bush and Chimayo (0.94) and the lowest between Tepin Guatemala and Black Hungarian (0.55). For FW, the mean IBS for small and large types was 0.70 ± 0.06. Most of the admixture occurred within small-sized hot peppers and large bell peppers indicating strong artificial selection for fruit size.

Figure 3. Individuals are ordered by their Euclidean distance (identity by state) and clustering with the tree is shown on top.

Figure 3

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Heat map key is presented on the top left corner (values rescaled from 0.6 to 1).

Population differentiation and signals of positive selection

The allele fixation index (FST) between domesticated and wild accessions was 0.10. The FST between low and high, low and medium, and medium and high capsaicin types was 0.08, 0.02 and 0.03, respectively, and that between small and large, small and medium, and medium and large FW types was 0.15, 0.03 and 0.07, respectively. The highest FSTwas noted for SNPs on chromosomes 1, 2, 4, 6, 7 and 8, so these regions are under positive selection. We annotated 122 regions showing strong positive selection and identified important genes for FW (Table S5). When comparing significant (P < 0.001) pairwise FST distribution of large and small FW accessions across the genome, we identified genomic areas with selective sweep signatures that are important for FW (Figs 4 and 5). A segment of 177 Mb was under strong selection sweep on chromosome 11. This sweep was from 34,758,394 to 211,919,750 Mb. In total, 659 genes located in this sweep area have important roles in transmembrane transport of lipids, intercellular carbohydrate transport, carbohydrate metabolic process and carbohydrate transport, ATP binding, flavonoid biosynthesis/auxin response, RNA splicing, nucleic acid binding protein, transcription regulation, glutathione metabolic process, positive regulation of GTPase activity, and other functions (Tables S6 and S7).

Figure 4. Genome-wide window-based pairwise FST values of low and high FW (blue) and overall FST values (red) across chromosomes.

Figure 4

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Note FST distribution on part of chromosome 11 showed distinct sweep.

Figure 5. Genome-wide window-based pairwise FST values of small and large fruit types (blue) and overall FST values (red) across chromosomes.

Figure 5

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Note FST distribution on part of chromosome 11 showed distinct sweep.

Analysis of LD

Haplotype distribution is important in comparing common and unique patterns of genetic variation of C. annuum gene pools and has a wide range of applications. The two major processes that shape haplotype structure are the domestication process and breeding history. We used “Minimize historical recombination”, a block-defining algorithm developed by Gabriel et al.21 to define haplotypes of various lengths. The upper confidence bound was set to 0.98 and the lower bound was set to 0.70. SNPs below MAF of 0.05 were skipped. Maximum block length was set to 160Kb. The EM (Expectation Maximization) algorithm was used for haplotype estimation with convergence tolerance 0.0001 and frequency threshold of 0.01. Maximum EM iterations were set to 50. The current study identified 1189 haplotypes containing 3413 SNPs with a range of 9 to 2 SNPs per haplotype (Table S8).We conducted an extensive LD analysis on the entire dataset of 94 C. annuum collections, on all adjacent marker pairs within a chromosome or within a haplotype block. The results provided values for both the expectation-maximization (EM) algorithm22 and composite haplotype method (CHM)23. R2 (squared-allele frequency correlations) and D’ (LD estimate) values for the EM and CHM methods are in Table S9. We created LD plots using marker-pair associations of adjacent SNPs within a chromosome, within a haplotype block, and within genes (Fig. 6A, B, and C). Length of individual LD blocks varied along chromosomes, with regions of high and low LD interspersed (Fig. 7). Pairwise LD was estimated by r2 and we compared the pattern of decay at different levels. First, with pair-wise analysis considering SNPs across chromosomes, we noted LD decay on average, with an average block size of 139 kb (Fig. 6A). Second, analysis based on adjacent SNPs within haplotypes revealed LD decay within 28 kb (Fig. 6B). We performed genomewide haplotype analysis and identified 1209 haplotypes (Table S10) Third, analysis of SNPs located in exons revealed mean LD decay within 1 kb (Fig. 6C). For LD analysis on chromosome 11, we noted that an entire region under sweep was also under high LD (Fig. 8). Genes under sweep and high LD included CA11g07400 (AP-1 complex subunit gamma-1 with the biological process of intracellular protein transport), with LD 10.2 kb, followed by CA11g09160 (ankyrin-like protein, an acyltransferase), with LD 4.9 kb, and CA11g09970 (flavonol synthase/flavanone 3-hydroxilase), with LD 3.3 kb (Table S7).

Figure 6. Marker associations (r2) across various chromosomes.

Figure 6

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EM analysis is carried for (A) adjacent individual SNPs, (B) adjacent haplotypes, and (C) SNPs located in individual genes.

Figure 7. High and low linkage disequilibrium (LD) block regions interspersed across the 12 C. annuum chromosomes.

Figure 7

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Figure 8. LD distribution across the 177 Mb sweep region specific to fruit weight identified on chromosome 11.

Figure 8

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GWAS to locate QTL for capsaicin and dihydrocapsaicin content

We used a GWAS with 7,331 SNPs to identify alleles that affect capsaicin and dihydrocapsaicin content (Fig. 7; individual SNP associations along with the details of major and minor allele frequencies and magnitude of associations are in Tables S10, S11, and S12; detailed annotations for all associated SNP markers are in Tables 1 and 2. We found 30 and 56 SNPs associated with capsaicin and dihydrocapsaicin content, respectively; 14 were common to both traits (Fig. 9). Average variation (%) explained per chromosome varied from 11.6 to 17.5 for capsaicin content and 12.9 to 16.9 for dihydrocapsaicin content.

Table 1. Annotation of significantly associated SNPs for capsaicin and dihydrocapsaicin content.

Trait/markers Locus1 Gene annotation Location of SNP Ma→Mi Amino acid # Molecular function Biological process
Capsaicin and dihydrocapsaicin
S1_31111874 CA01g09570 F-box/FBD/LRR-repeat protein Promoter C→G — Unknown function Regulation of axonogenesis
S3_211558976 CA03g19170 Mitochondrial carrier protein MTM1-like Exon 1 A→G V→I# Metallochaperone activity Manganese and phosphate ion transport
S5_215972421 CA05g15510 Laccase cupredoxin Exon 5 C→G T→S# Ferroxidase activity Seed germination and root elongation
S5_227837981 CA05g18080 Ankyrin repeat-containing protein Exon 1 A→G D→G# Acyltransferase, Transferase Cell growth regulation
S5_229634509 CA05g18740 IKI3 family protein Exon 3 A→T K→R# Histone acetyltransferase, tRNA binding Transcription and protein transport
S6_203416571 CA06g14430 ABC transporter G family Exon 20 C→T A→V# ATPase activity, coupled to transmembrane movement Transmembrane transport of lipids
S10_156251204 CA10g10170/CA10g10180 Zinc-finger CCHC type/GRAS transcription factor Intergenic G→A — Nucleic acid binding/DNA binding mRNA processing/Regulation of transcription
S10_172735351 CA10g10850 Nuclear transport factor 2 (NTF2) family protein Exon 1 T→C N→N Protein transport Nucleo-cytoplasm transport
S10_221317647 CA10g16820 4-hydroxy-tetrahydrodipicolinate synthase Intron 4 A→C — 4-hydroxy-tetrahydrodipicolinate synthase Lysine biosynthesis, diaminopimelate bisynthesis
S10_225598553 CA10g18180 Short-chain type alcohol dehydrogenase 3-UTR C→T — Oxidoreductase —
S11_83592400 CA11g09150 ABC transporter C family member 3-like Intron 1 A→T — ATPase activity, coupled to transmembrane movement Transmembrane transport of lipids
S11_85543247 CA11g09200/CA11g09210 Transparent Testa 12/F-box protein Intergenic C→T — DNA binding transcription factor/Protein binding Proanthocyanidin biosynthesis, seed development/-
S11_85543251 CA11g09200/CA11g09210 Transparent Testa 12/F-box protein Intergenic T→C — DNA binding transcription factor/Protein binding Proanthocyanidin biosynthesis, seed development/-
S11_85543257 CA11g09200/CA11g09210 Transparent Testa 12/F-box protein Intergenic A→G — DNA binding transcription factor/Protein binding Proanthocyanidin biosynthesis, seed development/-
Capsaicin only
S3_212689068 CA03g19340 Putative hydrolase Promoter T→C — Hydrolase activity Regulation of cell proliferation
S10_213596026 CA10g15030 Syntaxin-71-like (t-SNARE family) Intron 3 A→T — Protein transporter, SNAP receptor Vesicle transport, protein target to membrane
Dihydrocapsaicin only
S2_78953537 CA02g05900/CA02g05910 ATP-dependent DNA helicase pcrA/Peroxidase Intergenic A→C — ATP binding, DNA binding/metal ion binding, peroxidase activity DNA replication/lignin biosynthesis, H2O2 catabolism
S2_136027877 CA02g11920 Detected protein of unknown function Exon 8 C→G H→D# — —
S5_6535912 CA05g02820 Detected protein of unknown function Promoter C→T — — —
S5_30787082 CA05g06630/CA05g06640 Pentatricopeptide repeat protein/CCCH-type zinc finger protein Intergenic T→C — RNA binding/DNA binding Transit peptide processing/Negative regulation of transcription
S5_213819539 CA05g15030/CA05g15040 Intracellular transport USO-1 protein/Basic 7 S globulin 2 Intergenic C→G — Protein transporter activity/aspartic-type endopeptidase activity SNARE complex and vesicles docking/-
S6_107738639 CA06g07610/CA06g07620 F-Box protein/Elongation factor 1-alpha Intergenic C→G — Glycoprotein binding/translation elongation, GTPase activity DNA repair, protein ubiquination/Protein biosynthesis
S8_142512369 CA08g18030/CA08g18040 Serine/threonine-protein kinase SMG1/Serine/threonine-protein kinase SMG1-like Intergenic G→A — ATP, metal ion binding/ATP, metal ion binding mRNA transport, response to stress/mRNA transport, response to stress
S9_220486511 CA09g12880 Os09g0132600 protein Exon 4 C→G H→D# Uncharacterized protein —
S11_249688869 CA11g16730/CA11g16740 Nectarin 1/Disease resistant protein BS2 Intergenic A→G — Manganese ion binding, SOD activity/Nucleotide binding Nutrient reservoir activity/disease resistance
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1Korea genome locus number; + or −, direction of transcription on + or – strand; Ma→Mi - Major and minor alleles from mapping population; #nonsynonymous mutation.

Table 2. Annotation of significantly associated SNPs for fruit weight.

Trait/markers Locus1 Gene annotation Location of SNP Ma→Mi Amino acid # Molecular function Biological process
Fruit weight (2011 and 2012)
S1_178148471 CA01g23190 Isopenicillin N epimerase (AAT_I superfamily) Exon 1 C→T S→N# ADP binding, catalytic activity Penicillin biosynthesis
S1_178214095 CA01g23200 protein transport protein SEC23-like (zf, MIDAS domain) Promoter A→G — Zinc ion binding Intracellular protein transport
S2_169874314 CA02g30530/CA02g30540 Na+/H+ antiporter/Glucose-6-phosphate 1-dehydrogenase Intergenic C→T — Sodium:proton antiporter activity/NADP binding Multiple cellular processes/glucose metabolic process
S3_230322338 CA03g24610 SNF1-related protein kinase/RAD50-interacting protein Intron 4 C→T — ATP binding, protein kinase/membrane traffic between the Golgi and ER Nitrate assimilation, phosphorylation, carbohydrate metabolism/protein transport and Golgi transport
S3_230372266 CA03g24640 Ubiquitin-like modifier-activating enzyme 5-like (thiamine synthesis) Intron 10 A→T — Cofactor binding Small protein activating enzyme activity
S5_131824978 CA05g10770 Unknown protein Promoter C→T — — —
S6_202147247 CA06g14190/CA06g14200 STYLOSA protein/Flavin monooxygenase Intergenic C→T — Auxin transporter inhibitor/NADP binding Regulation of floral organ identity/glucosinolate biosynthesis
S6_202147285 CA06g14190/CA06g14200 STYLOSA protein/Flavin monooxygenase Intergenic G→A   Auxin transporter inhibitor/NADP binding Regulation of floral organ identity/glucosinolate biosynthesis
S6_202147337 CA06g14190/CA06g14200 STYLOSA protein/Flavin monooxygenase Intergenic C→→T   Auxin transporter inhibitor/NADP binding Regulation of floral organ identity/glucosinolate biosynthesis
S6_202147420 CA06g14190/CA06g14200 STYLOSA protein/Flavin monooxygenase Intergenic C→T   Auxin transporter inhibitor/NADP binding Regulation of floral organ identity/glucosinolate biosynthesis
S6_227195619 CA06g22610 Chloroplastic- FAF-like protein Exon 1 C→G N→K# — —
S8_132459145 CA08g12350 DnaQ-like exonuclease Intron 2 C→T — DNA binding Exonuclease activity
S9_250224149 CA09g16860 Mitochondrial-processing peptidase subunit alpha Intron 11 C→T — Metal ion binding Processing proteins targeting to mitochondrion
S10_229225552 CA10g19740 Cell division control protein 45 (CDC45) Exon 1 A→G S→S Chromatin binding, helicase activity Cell division, DNA replication
S11_94177155 CA11g09530 Clathrin assembly protein Promoter A→C   low-density lipoprotein particle receptor binding Intracellular protein transport, endocytosis
S12_72971688 CA12g10020/CA12g10030 CLAVATA1 receptor kinase/Pentatricopeptide repeat Intergenic G→T   Protein kinase, ATP binding/RNA binding Regulation of meristem structural organization, cell differentiation/Transit peptide processing
Fruit weight 2011 only
S6_204245052 CA06g14620 TRS120 isoform Intron G→A   Cell plate assembly Cell division
S6_204246361 CA06g14620 TRS120 isoform Exon 6 G→A R→G# Cell plate assembly Cell division
S10_231176974 CA10g20890/CA10g20900 Unknown function/Transcription factor Intergenic T→C   -/DNA binding -/Transcription
Fruit weight 2012 only
S4_215751345 CA04g19880/CA04g19890 LIM domain containing protein/DNA damage-binding protein Intergenic A→G   DNA and zinc ion binding/damaged DNA binding Regulation of transcription/protein ubiquitination, nucleotide excision repair
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1Korea genome locus number; + or −, direction of transcription on + or − strand; Ma→Mi - Major and minor alleles from mapping population; #nonsynonymous mutation.

Figure 9. Manhattan plot of the genome-wide association study for fruit weight and capsaicinoids (capsaicin and dihydrocapsaicin).

Figure 9

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Chromosome coordinates are displayed along the X-axis, with the negative log-10 of the association P-value for each SNP on the Y-axis. Higher negative log-10 indicates stronger association with the trait. Venn diagrams are of the unique and common significantly associated SNPs for capsaicin and dihydrocapsaicin content and fruit weight in 2011 and 2012.

Significantly associated SNPs for both capsaicin and dihydrocapsaicin content were S1_31111874 (-log10 P = CA 6.6 and DCA 6.9), S3_211558976 -log10 P = CA 4.0 and DCA 3.3), S5_215972421 (-log10 P = CA 3.6 and DCA 3.9), S5_227837981 (-log10 P = CA 3.4 and DCA 3.8), S5_229634509 (-log10 P = CA 3.6 and DCA 4.5), S6_203416571 (-log10 P = CA 3.9 and DCA 3.5), S10_156251204 (-log10 P = CA 3.0 and DCA 5.8), S10_172735351 (-log10 P = CA 3.1 and DCA 4.0), S10_221317647 (-log10 P = CA 4.0 and DCA 3.9), S10_225598553 (-log10 P = CA 3.9 and DCA 3.5), S11_83592400 (-log10 P = CA 3.4 and DCA 3.7), S11_85543247 (-log10 P = CA 4.2 and DCA 6.3), S11_85543251 (-log10 P = CA 3.6 and DCA 5.3), and S11_85543257 (-log10 P = CA 4.2 and DCA 6.3).

GWAS to locate QTL for FW

Despite the high variation noted for FW across the 2 years of the study, 15 common SNPs were found strongly associated (Fig. 8, Table 2, S13 and S14). Our GWAS revealed 28 and 33 SNPs with strong association during 2011 and 2012, respectively. We found an association of S1_178148471 (-log10 P 2011 = 5.2 and 2012 = 4.0) located in sopenicillin N epimerase (AAT_I superfamily) with ADP binding catalytic activity, S1_178214095 (-log10 P 2011 = 5.4 and 2012 = 4.6) of the protein transport protein SEC23-like (zf, MIDAS domain) that regulates Zinc ion binding, S2_169874314 (-log10 P 2011 = 4.0 and 2012 = 6.5) located in the intergenic space of Na+/H+ antiporter and lucose-6-phosphate 1-dehydrogenase, S3_230322338 (-log10 P 2011 = 3.3 and 2012 = 3.9) of the intergenic space between SNF1-related protein kinase and RAD50-interacting protein S3_230372266 (-log10 P 2011 = 3.5 and 2012 = 3.1) located in Ubiquitin-like modifier-activating enzyme 5-like (thiamine synthesis) and S5_131824978 (-log10 P 2011 = 3.9 and 2012 = 3.9) of an unknown protein. We also found an association of S6_202147247 (-log10 P 2011 = 3.9 and 2012 = 3.9), S6_202147285 (-log10 P 2011 = 3.1 and 2012 = 3.2), S6_202147337 (-log10 P 2011 = 3.1 and 2012 = 3.2) and S6_202147420 (-log10 P 2011 = 3.1 and 2012 = 3.2) located in the intergenic space between STYLOSA protein and flavin monooxygenase in both years. We found an association of S6_227195619 (-log10 P 2011 = 3.9 and 2012 = 3.8) of chloroplastic-FANTASTIC FOUR (FAF)-like protein, S8_132459145 (-log10 P 2011 = 6.8 and 2012 = 3.7) of DnaQ-like exonuclease, S9_250224149 (-log10 P 2011 = 6.8 and 2012 = 3.7) of mitochondrial-processing peptidase subunit alpha, S10_229225552 (-log10 P 2011 = 3.1 and 2012 = 5.0) of cell division control protein 45 (CDC45), S11_94177155 (-log10 P 2011 = 3.8 and 2012 = 3.0) of Clathrin assembly protein, and S12_72971688 (-log10 P 2011 = 7.06 and 2012 = 3.9) in the intergenic space between CLAVATA1 receptor kinase and pentatricopeptide repeat. S6_227195619, S6_204246361, S10_229225552 were nonsynonymous SNPs located in isopenicillin N epimerase (AAT_I superfamily), chloroplastic-FAF-like protein, cell division control protein 45 (CDC45) and TRS120 isoform, respectively, which have biological processes involving cell division and meristem organization.

Discussion

Understanding the genetic control of traits influenced by domestication is improving as a result of GWAS for several crops. Domesticated peppers have larger fruits than wild peppers but also have larger leaves, flowers and seeds. An overall increase in size of many different organs could result from an increase in cell number or size or both24. Principal component analysis (PCA), model based population structure and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions were in agreement with capsaicin content (CA) and FW classifications indicating the importance of these traits in shaping modern pepper genome. Our study focused on unraveling various mechanisms underlying fruit weight and capsaicin content among C. annuum peppers.

A total of 659 genes located in the sweep of chromosome 11 were identified that influenced FW in C. annuum. In particular, the pentatricopeptide repeat protein and ABC transporter are known genes for tomato FW25, and the ankyrin repeat protein, which functions as an acyltransferase, with a homologue on chromosome 5 highly associated with capsaicin content as well as FW are located in the sweep region. Similarly, recent tomato genome analysis revealed that most of the genes, namely glutathione S-transferase, actin-related protein 2/3 complex, endo-1, 4-beta-glucanase, RCC1 domain-containing protein, ankyrin repeat protein, and xanthine dehydrogenase, were also found in the chromosome sweep important for tomato domestication26. We identified 30 genes in the sweep region with high LD, and our GWAS revealed highly significant markers for FW within the sweep. Qin et al.9 identified 115 regions across the genome containing 511 genes that are important for domestication with strong selective sweep signals by using WGS analysis. Among the genes in the chromosome 11 sweep, ankyrin-like protein, an acyltransferase, showed extended LD, up to 10 kb, which implies its role in pepper fruit weight.

Despite a number of genes involved in the capsaicin synthesis pathway per se, these genes need upstream and trans-regulators for proper spatiotemporal expression during capsaicin synthesis in pepper fruit formation. Our GWAS results showed an association with multiple genes via tightly linked SNP markers. Among the DNA/RNA binding proteins, CCHC zinc-finger, CCCH zinc-finger, GRAS transcription factor, transparent testa 12, and pentatricopeptide repeat protein are the major markers. Because these genes are transporters, transcription factors and catalytic enzymes, they might be regulators of the genes in the capsaicin biosynthesis pathway. Another homologue of ankyrin-like protein on chromosome 5 was also strongly associated with capsaicinoid content. Han et al.27, Stewart et al.28 and Reddy et al.29 demonstrated that Pun1 is responsible for capsaicinoid synthesis; the authors further suggested the presence of an unknown enzyme that reduces vanillin to vanillyl alcohol. Pun1 located on chromosome 2 was noted to encode AT3, an acyl transferase from the BAHD acyl transferase superfamily. How AT3 is related to the acyltransferase on chromosome 11 and 5 needs further investigation. Because its molecular function is also as an acyltransferase, ankyrin repeat-containing protein might function as an additional Pun1 gene, which is yet to be determined, or it might have an accessory role in capsaicin synthesis. Our results demonstrating the influence of multiple chromosomal regions on capsaicinoid content may begin to explain the extensive diversity evident in pepper for capsaicinoid concentration in pungent genotypes.

We identified 16 SNPs strongly associated with FW in both years of the study. The C. annuum progenitor species bear fruit of much smaller size than do the cultivated counterparts. Important findings from our FW GWAS study reveal similar biological function in tomato and other plants (Lin et al.38). We found a strong association of Stylosa protein (S6_202147247 S6_202147285 S6_202147337 S6_202147420) with FW in both seasons of the study; FASCIATED (FAS), encoded by a member of the YABBY family regulating organ polarity, is thought to play an important role in plant growth and development30,31. FAS controls fruit shape in tomato32. Earlier, STYLOSA (STY) was found to regulate floral homeotic meristem and organ identity in Antirrhinum33. Interactions between STYLOSA and YABBY family proteins control Antirrhinum vegetative and reproductive development34. The interaction between STYLOSA (Ca06g14190) and YABBY might be critical for fruit size/shape and weight in pepper.

S6_227195619 causes a nonsynonymous mutation in chloroplastic FAF protein and we found it strongly linked with FW in both seasons of the study. Plastid genes are expressed at high levels in photosynthetically active chloroplasts, including in developing fruits. Chloroplastic-FAF protein regulates shoot meristem size in Arabidopsis. FAF genes are expressed in the center of the shoot meristem, overlapping with the site of WUSCHEL (WUS) expression. Strong interaction between FAF and WUS determine the fate of meristem activity35. Hence, FAF (Ca06g22610) might regulate the size of the shoot meristem as well as FW by modulating the CLV3-WUS feedback loop in pepper. A significantly associated SNP, S9_250224149, was found in the mitochondrial processing peptidase alpha subunit (Ca09g16860), which might be important for fruit development because its ortholog in tomato is specifically and differentially expressed during cell expansion stages in early stages of fruit development36.

S12_72971688 is an intergenic SNP close to CLAVATA 1 receptor kinase that showed a strong association with FW in both seasons. Arabidopsis plants homozygous for mutations at the CLAVATA1 (CLV1) locus, a receptor kinase protein, accumulate excess undifferentiated cells37,38. This gene is critical for shoot and flower meristem size. In our study, Ca12g10020, or CLAVATA1 receptor kinase, might interact with CLV3 as a ligand–receptor pair in a signal transduction pathway coordinating growth between adjacent meristematic regions and controlling the balance between meristem cell proliferation and differentiation.

Fine mapping of the QTL fw3.2 controlling FW in tomato was accomplished recently25 and genes in this QTL range were identified. Among seven putative genes identified in this region, ORF4 encodes a protein with high identity to PNM1 in Arabidopsis PNM1 belongs to the pentatricopeptide repeat containing protein (PPR) family that functions in RNA binding (Hammani et al. 2011). The marker S12_72971688 linked to the locus Ca12g10030 (PPR) might play key roles in determining FW in pepper as QTL fw3.2 does in tomato.

Given our SNP density and sample size, this study is not sufficiently robust to find alleles of small effect among the pepper secondary centers of origin distributed across the world. However, we located SNPs with major effect in highly inbred, diverse and smaller population. Some of the strongest signals are quite far from known capsaicin genes possibly because of ascertainment bias. Also SNPs located in the candidate genes may not be in LD, which hampers their identity in association mapping strategies. Furthermore, stringent control for population stratification and IBS may eliminate useful SNPs located in the candidate genes. Such tradeoffs are part of GWAS, especially in reducing spurious associations39. Zhao et al.39 and Rife et al.40 proposed that SNP identification from transcriptome datasets or spiked GBS, which combines targeted amplicon sequencing with reduced representation GBS, will improve our ability to detect moderate-strength and rare alleles, especially those located in candidate genes. Analogous approaches have been reported39,41,42,43.

Our GWAS for capsaicin and dihydrocapsaicin content and FW identified SNPs located in the candidate genes known to have similar biological functions in tomato and other plants for these domestication related traits. Accessions containing higher minor allele frequencies from this study can be used to generate nested association mapping populations to validate GWAS results and further dissect the complex interaction among genes involved in the pleotropic effects on fruit size and capsaicin content evident in Capsicum.

Materials and Methods

We included 94 accessions of C. annuum belonging to various countries representing a wide geographical area of the world for the molecular diversity analysis (Table S1). These selfed accessions were grown in three replications during two seasons (2011 and 2012) adapting a row-to-plant spacing of 100 × 30 cm. Ten plants per accession were grown in each replication. FW (g), was collected for five plants. Quantitative analysis of capsaicin and dihydrocapsaicin content was performed using greenhouse-grown plants in three replications using the 1200 series HPLC system (Agilent Technologies, Santa Clara, CA) with a degasser, an autosampler, and a binary pump as described7.

Genotyping by sequencing

Genomic DNA was isolated using the DNeasy plant mini kit (QIAGEN, Germany), and GBS was as described44,45. Briefly, genome complexity was reduced by digesting total genomic DNA from individual samples with the ApeKI, a type II restriction endonuclease that recognizes a degenerate 5-bp sequence (GCWGC, where W is A or T), which creates a 5′ overhang (3 bp) and is partially methylation-sensitive (will not cut if the 3′ base of the recognition sequence on both strands is 5-methylcytosine). Digested products were then ligated to adapter pairs with enzyme-compatible overhangs; one adapter contained the barcode sequence and a binding-site Illumina sequencing primer (Illumina Inc., USA). These samples were pooled, purified and amplified with primers compatible with the adapter sequences. Temperature cycling was 72 °C for 5 min, 98 °C for 30 s followed by 18 cycles of 98 °C for 30 s, 65 °C for 30 s, and 72 °C for 30 s with a final Taq extension step at 72 °C for 5 min. Amplified sample pools constituted a sequencing “library”. Libraries were purified and 1 μL was loaded onto an Experion automated electrophoresis station (BioRad, Hercules, CA) for evaluation of fragment sizes. Libraries were considered suitable for sequencing if adapter dimers (~128 bp in length) were minimal or absent and most of the other DNA fragments were between 170 and 350 bp. If adapter dimers were present in excess of 0.5% (based on the Experion output), libraries were constructed again by using a few DNA samples and decreasing adapter amounts. The PCR primers also added 3′ sequences complementary to the solid-phase oligonucleotides that coat the Illumina sequencing flow-cell. After PCR, pooled products were purified; GBS “library” fragment size distributions were checked on a BioAnalyzer (Agilent Technologies, USA). Products were quantified and diluted for sequencing by use of Illumina HiSeq 2500. A bioinformatics pipeline, TASSEL-GBS, designed for efficient processing of raw GBS sequence data into a SNP genotype file46 was used. Barcoded sequence reads were processed and collapsed into a set of unique sequence tags, with one TagCounts file produced per input FASTQ. Chromosomal assignment physical map position of candidate genes and GBS markers, were deduced from the hot pepper WGS draft at http://peppergenome.snu.ac.kr. SNPs were designated on the basis of chromosome number and position (e.g., S10_172735351 indicates SNP located at 172735351 position on chromosome 10).

Data Analysis

Population structure analysis

For quantitative assessment of the number of clusters in the GWAS panel, we used a Bayesian clustering analysis with a model-based approach implemented in STRUCTURE v2.247. This approach involves use of multi-locus genotypic data to assign individuals to clusters or groups (K) without prior knowledge of their population affinities. The program was run with SNP markers for k-values 1–9 (hypothetical number of subgroups), with 100,000 burn-in iterations, followed by 500,000 Markov Chain Monte Carlo (MCMC) iterations for accurate parameter estimates with a high-performance cluster. To verify the consistency of the results, we performed three independent runs for each K. An admixture model with correlated allele frequencies was used. The optimal K value was determined by use of an ad-hoc statistic, ΔK. The number of Ks in each dataset was evaluated by ΔK values estimated and visualized with the software Structure Harvester, (www.taylor0.biology.ucla.edu/structureHarvester)48. To facilitate the interpretation of population-genetic clustering results, we used CLUMPP (CLUster Matching and Permutation Program)49, which groups individuals into populations on the basis of multilocus genotypes, and the output was directly input into a program for cluster visualization DISTRUCT 1.150. In a second approach, we used principle component analysis (PCA) with the SNP & Variation Suite (SVS v8.1.5) (Golden Helix, Inc., Bozeman, MT, USA; www.goldenhelix.com).

Analysis of population differentiation

Fixation index (FST) estimation was based on Wright’s F statistic51 in SVS v8.1.5 (http://goldenhelix.com/). Annotation and gene ontology terms for genes from the selective sweeps were identified with the WGS draft at http://peppergenome.snu.ac.kr.

GWAS mapping

For GBS data, we considered only SNPs successfully mapped to the Capsicum WGS draft, because knowing the chromosome location of SNPs helps prevent spurious LD and thereby unreliable association mapping. Before studying LD decay, haplotype blocks were calculated for all markers using the default settings in SVS v8.1.5. Adjacent and pairwise measurements of LD for GBS data were calculated separately for SNPs in each chromosome. All LD plots and LD measurements and haplotype frequency calculations involved use of SVS v8.1.5 and Tassel 5.0. For GWAS, the population structure Q matrix was replaced by the PC matrix52. The PC matrix and identity by descent (IBD) was calculated from LD-pruned SNPs in SVS v8.1.5. GWAS involved a single-locus mixed linear model developed by the EMMAX method53 and implemented in SVS v8.1.5. We used a PC matrix (first two vectors) to correct for population stratification and the IBD matrix to correct polygenic background. Manhattan plots for associated SNPs were visualized in GenomeBrowse v1.0 (Golden Helix, Inc). The SNP P-values from GWAS underwent sequential Bonferroni correction54 as well as false discovery rate (FDR) analysis55. Annotation and gene ontology terms for the SNP containing sequences were identified with the WGS draft at http://peppergenome.snu.ac.kr.

Additional Information

How to cite this article: Nimmakayala, P. et al. Genome-wide diversity and association mapping for capsaicinoids and fruit weight in Capsicum annuum L. Sci. Rep. 6, 38081; doi: 10.1038/srep38081 (2016).

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Material

Supplementary Information
srep38081-s1.doc (47.5KB, doc)
Suplimentary Tables
srep38081-s2.xls (1.1MB, xls)

Acknowledgments

The study received funding from USDA-NIFA (2010-02419), NSF-EPSCOR#09-570 - EPS-1003907, NIH Grant P20RR016477 to the West Virginia IDeA Network for Biomedical Research Funding and the Gus R. Douglass Institute (graduate research assistantship to V.A., K.T., L.Y. and B.D.). Doil Choi was supported by the Agricultural Genome Center of Next Generation Biogreen 21 program (PJ011275-01), RDA of Korean government.

Footnotes

Author Contributions U.R., J.S., G.H., R.H. and P.N. designed the study and drafted the manuscript. P.N., T.S., V.A., G.V., K.T., L.Y., J.D., S.A., A.A., B.D. and M.N. generated field and capsaicinoid phenotyping. P.N., T.S., V.A., G.V., K.T., L.Y., J.D., A.A. and B.D. extracted DNA and assisted to generate genome-wide SNPs. M.P., S.M. and D.C. provided whole genome sequence draft and mapped SNPs to the genome. U.R., P.N., T.S., and V.A. performed GWAS analysis.

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Supplementary Materials

Supplementary Information
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srep38081-s2.xls (1.1MB, xls)

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