Fruit Shape Traits Research Articles

Exploration into natural variation for genes associated with fruit shape and size among Capsicum chinense collections

Phenotype diversity within cultivated Capsicum chinense is particularly evident for fruit shape and size. We used this diversity in C. chinense to further unravel the genetic mechanisms underlying fruit shape variation in pepper and related Solanaceous species. We identified candidate genes for C. chinense fruit shape, explored their contribution to population structure, and characterized their potential function in pepper fruit shape. Using genotyping by sequencing, we identified 43,081 single nucleotide polymorphisms (SNPs) from diverse collections of C. chinense. Principal component, neighbor-joining tree, and population structure analyses resolved 3 phylogenetically robust clusters associated with fruit shapes. Genome-wide association study (GWAS) was used to identify associated genomic regions with various fruit shape traits obtained from image analysis with Tomato Analyzer software. In our GWAS, we selected 12 SNPs associated with locule number trait and 8 SNP markers associated with other fruit shape traits such as perimeter, area, obovoid, ellipsoid and morphometrics (5y, 6y and 7y). The SNPs in CLAVATA1, WD-40, Auxin receptor, AAA type ATPase family protein, and RNA polymerase III genes were the major markers identified for fruit locule number from our GWAS results. Furthermore, we found SNPs in tetratricopeptide-repeat thioredoxin-like 3, enhancer of ABA co-receptor 1, subunit of exocyst complex 8 and pleiotropic drug resistance proteins associated with various fruit shape traits. CLAVATA1, WD-40 and Auxin receptor genes are known genes that affect tomato fruit shape. In this study, we used Arabidopsis thaliana T-DNA insertion knockout mutants and expression profiles for functional characterization of newly identified genes and to understand their role in fruit shape.

Fruit shape morphometric analysis and QTL detection in a set of eggplant introgression lines

Eggplant fruit shape is an important quantitative agronomic trait. The use of introgression lines (ILs) for QTLs identification is a powerful tool for the elucidation of the genetic control of eggplant fruit shape. In the present study, a set of 16 eggplant ILs, each harboring a single marker-defined chromosomal segment from the wild eggplant relative S. incanum in the genetic background of S. melongena, was evaluated for fruit shape in two environments (open field and screenhouse). A detailed phenotyping of the fruits of the two parents, hybrid and ILs was performed using 32 morphological descriptors of the phenomics tool Tomato Analyzer. Several morphological differences were found between parents, and the hybrid displayed negative heterosis for many fruit shape traits, being more similar to the S. incanum parent. Significant differences for most fruit shape descriptors were found between ILs and the recipient parent. For many descriptors, the genotype factor had the highest contribution to the percentage of the sum of squares. Although the contributions of the environment and the G × E interaction were significant for almost all descriptors, their effects on fruit shape were relatively low. Hierarchical clustering revealed nine clusters of highly correlated traits and six ILs groups. A total of 41 stable QTLs spread over ten chromosomes were detected. Of these, twenty QTLs associated to Basic Measurement and Fruit Shape Index descriptors were syntenic to other previously reported in several intraspecific and interspecific eggplant populations, while twenty-one QTLs, including Blockiness, Homogeneity, Asymmetry and Internal Eccentricity, were new. In addition, mutations associated to genes belonging to SUN, OVATE and YABBY families described in tomato were reported in the QTLs genomic regions identified in eggplant. Eleven SUN and YABBY genes were proposed as potential candidate controlling fruit shape variations in eggplant. Our results provide novel and highly relevant insights on the genetics of fruit shape in eggplant and have important implications for eggplant breeding.

Dynamic Changes of Fruit Shape Traits and Its Correlation to the Morphology of Other Organs in Cucumber

Fruit shape and size are important assessment parameters to evaluate and classify accessions in cucumber breeding. Clarifying the relations of the shape and size of commodity fruits or mature fruits to that of other organs, like seed, leaf, flower and so on, is significant for multitype breeding of cucumber fruit. It can help breeders to predict the shape and size of a cucumber fruit in the early selection and shorten the breeding cycle. In this study, the dynamic morphological observation of fruit length (FL), fruit diameter (FD) and the fruit shape index (FSI) of developing cucumber fruits in different types and the correlation of fruit shape indexes between fruit and other organs were investigated. The results showed that 28 cucumber accessions with different shape and size were classified into four types, namely long fruits, medium long fruits, medium fruits and short fruits. The comparative analysis of FL and FD among different types and different development stages of cucumber fruits showed that the development of FL and FD were both consistent with the model “S” curve, slow–fast–slow, and there existed strong positive correlation between their growth. During fruit development, the shape index was highly positively correlated among ovary, commodity fruit and mature fruit. Besides, both the length and width of cotyledon, true leaf and female flower petal were positively correlated to the FL of commodity fruit. The length and width of seed, length of ovary carpopodium and pedicel length were also positively correlated to the FD of commodity fruit. For seed, cotyledon and true leaf, no correlation was found between their shape index and their FSI.

Markers for selection of three alleles of ClSUN25-26-27a (Cla011257) associated with fruit shape in watermelon

Fruit shape is an economically important trait in many horticultural crops. The genes and mechanisms underlying fruit shape variation are poorly understood in watermelon. A deletion (DEL) in ClSUN25-26-27a (Cla011257), a member of the SUN gene family, has been shown to be associated with elongated fruit. In the current study, we sequenced ClSUN25-26-27a in three watermelon cultivars with different fruit shape indices (FSIs). A novel allele containing a non-synonymous point mutation in exon 3 was identified in Klondike Black Seeded. KASP assays (ClSUN-1 and ClSUN-2) were developed to distinguish three ClSUN25-26-27a alleles (WT, KBS, and DEL), and their effects on ovary and fruit shape traits were determined in a cultivar panel and segregating populations. The different alleles showed a significant association with ovary and fruit length and shape as well as the angles of the distal and proximal ends. These effects were primarily pre-anthesis. The KASP assays can serve as tools for marker-assisted selection (MAS) of fruit length and shape in watermelon. This study highlights the allelic variation in ClSUN25-26-27a and its association with fruit shape in watermelon.

Genetic analysis and QTL mapping of fruit length and diameter in a cucumber (Cucumber sativus L.) recombinant inbred line (RIL) population

Fruit length and diameter are very important appearance quality which affects preference of consumers and quality of fruit. To improve the genetic mechanisms of cucumber fruit shape and size, an F2:5 recombinant inbred line (RIL)-population was derived from a cross between Q16 inbred lines which had slender fruit and Q24 inbred lines which had round fruit to screen fruit shape QTLs locus. 85 RILs, 15 F1 and 15 of each parental line were grown in the spring of 2016 and 2017 respectively. The length and diameter of ovary, immature fruit and mature fruit were measured at blooming day, 12 days after pollination and 35 days after pollination respectively. The RIL population was screened basing on the data related fruit using 89 SSR markers and 1 InDel marker. Twenty-one QTLs loci were totally identified for fruit shape traits from RIL population. Comparing the flanking markers of 21 QTL loci allowed to 5 consensus QTLs FS1.1, FS1.2, FS2.1, FS3.1 and FS6.1 loci, in which FS3.1 played a role in fruit elongation, FS6.1 was important for the increase of fruit diameter, and the else 3 QTLs acted in both fruit elongation and diameter. The results from this study may increase the understanding of the genetic basis control of fruit shape and size and provide support for marker-assisted selection in cucumber with ideal fruit shape.

Phenotyping of Eggplant Wild Relatives and Interspecific Hybrids with Conventional and Phenomics Descriptors Provides Insight for Their Potential Utilization in Breeding.

Eggplant (Solanum melongena) is related to a large number of wild species that are a source of variation for breeding programmes, in particular for traits related to adaptation to climate change. However, wild species remain largely unexploited for eggplant breeding. Detailed phenotypic characterization of wild species and their hybrids with eggplant may allow identifying promising wild species and information on the genetic control and heterosis of relevant traits. We characterizated six eggplant accessions, 21 accessions of 12 wild species (the only primary genepool species S. insanum and 11 secondary genepool species) and 45 interspecific hybrids of eggplant with wild species (18 with S. insanum and 27 with secondary genepool species) using 27 conventional morphological descriptors and 20 fruit morphometric descriptors obtained with the phenomics tool Tomato Analyzer. Significant differences were observed among cultivated, wild and interspecific hybrid groups for 18 conventional and 18 Tomato Analyzer descriptors, with hybrids generally having intermediate values. Wild species were generally more variable than cultivated accessions and interspecific hybrids displayed intermediate ranges of variation and coefficient of variation (CV) values, except for fruit shape traits in which the latter were the most variable. The multivariate principal components analysis (PCA) reveals a clear separation of wild species and cultivated accessions. Interspecific hybrids with S. insanum plotted closer to cultivated eggplant, while hybrids with secondary genepool species generally clustered together with wild species. Many differences were observed among wild species for traits of agronomic interest, which allowed identifying species of greatest potential interest for eggplant breeding. Heterosis values were positive for most vigor-related traits, while for fruit size values were close to zero for hybrids with S. incanum and highly negative for hybrids with secondary genepool species. Our results allowed the identification of potentially interesting wild species and interspecific hybrids for introgression breeding in eggplant. This is an important step for broadening the genetic base of eggplant and for breeding for adaptation to climate change in this crop.

Construction of a genetic linkage map of watermelon (Citrullus lanatus) using CAPS and SSR markers and QTL analysis for fruit quality traits

A genetic map of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] was constructed using an F2:3 segregating population consisting of 145 individuals, which were derived from a cross between a cultivated inbred line (garden female parent) from China and an American inbred line (LSW-177). The map contained 125 polymorphic markers, comprising 82 cleavage amplified polymorphic sequence (CAPS) markers and 43 simple sequence repeat (SSR) markers. The map contained 11 major and 3 minor linkage groups spanning a total length of 1,244.5cM, with an average of 9.96cM between markers. All of the CAPS markers were newly developed based on high-throughput re-sequencing data for the garden female parent and LSW-177. A quantitative trait locus (QTL) analysis was conducted using the composite interval mapping method to locate fruit sugar content and fruit shape traits. A total of 10 QTLs were identified; 4 for fruit sugar content and 6 for fruit shape. This map and QTL analysis will be useful for breeding to improve various economic traits in watermelon.

Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus).

An intraspecific genetic map for watermelon was constructed using an F2 population derived from ‘Arka Manik’ × ‘TS34’ and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits.

Developmental genetic analysis of fruit shape traits under different environmental conditions in sponge gourd (Luffa cylindrical (L) Roem. Violales, Cucurbitaceae)

Analysis of genetic main effects and genotype × environment (GE) interaction effects for the fruit shape traits fruit length and fruit circumference in the sponge gourd (Luffa cylindrical (L) Roem. Violales, Cucurbitaceae) was conducted for diallel cross data from two planting seasons. A genetic model including fruit direct effects and maternal effects and unconditional and conditional variances analysis was used to evaluate the development of the fruit at four maturation stages. The variance analysis results indicated that fruit length and circumference were simultaneously affected by fruit direct genetic effects and maternal effects as well as GE interaction effects. Fruit direct genetic effects were relatively more important for both fruit shape traits during the whole developmental period. Gene activation was mostly due to additive effects at the first maturation stage and dominance effects were mainly active during the other three stages. The fruit shape trait correlation coefficients due to different genetic effects and the phenotypic correlation coefficients varied significantly for the various maturation stages. The results indicate that it is relatively easy to improve the two fruit shape traits for market purposes by carefully selecting the parents at the first maturation stage 3 days after flowering instead of at fruit economic maturation.

Genetic analysis of fruit shape traits at different maturation stages in sponge gourd

The fruit shape is important quantitative trait closely related to the fruit quality. However, the genetic model of fruit shapes has not been proposed. Therefore, in the present study, analysis of genetic effects for fruit shape traits (fruit length and fruit perimeter) in sponge gourd was conducted by employing a developmental genetic model including fruit direct effects and maternal effects. Analysis approaches of unconditional and conditional variances were applied to evaluate the genetic behavior of fruit shape traits at economical and physiological maturation times. The results of variance analysis indicated that fruit length and fruit perimeter were simultaneously affected by fruit direct genetic effects and maternal effects. Fruit direct genetic effects were relatively more important for fruit shape traits at whole developmental period. The gene expression was most active at the economical maturation stage (1 approximately 12 d after flowering) for two shape traits, and the activation of gene was mostly due to direct dominance effects at physiological maturation stage (13 approximately 60 d after flowering). The coefficients due to different genetic effects, as well as the phenotypic correlation coefficients, varied significantly between fruit shape traits themselves at various maturation stages. The results showed that it was relatively easy to improve fruit shape traits for industrial purpose by carefully selecting the parents at economical maturation stage instead of that at physiological maturation stage.

Morphological variation in tomato: a comprehensive study of quantitative trait loci controlling fruit shape and development

Variation in fruit morphology is a prevalent characteristic among cultivated tomato. The genetic and developmental mechanisms underlying similarities and differences in shape between the fruit of two elongated tomato varieties were investigated. Fruit from two F2 populations constructed from either Solanum lycopersicum cv. Howard German or cv. Banana Legs crossed with S. pimpinellifolium accession LA1589, and one BC1 population constructed with S. lycopersicum Howard German as the recurrent parent, were analysed for shape by using a new software program Tomato Analyzer. Quantitative trait loci (QTLs) controlling 15 individual shape attributes were mapped by both single and multitrait composite interval mapping in each population. In addition, principal components analysis and canonical discriminant analysis were conducted on these shape attributes to determine the greatest sources of variation among and between the populations. Individual principal components and canonical variates were subjected to QTL analysis to map regions of the genome influencing fruit shape in the cultivars. Common and unique regions, as well as previously known and novel QTLs, underlying fruit morphology in tomato were identified. Four major loci were found to control multiple fruit shape traits, principal components, and canonical variates in the populations. In addition, QTLs associated with the principal components better revealed regions of the genome that varied among populations than did the QTL associated with canonical variates. The QTL identified can be compared across additional populations of tomato and other fruit-bearing crop species.

Development of a Controlled Vocabulary and Software Application to Analyze Fruit Shape Variation in Tomato and Other Plant Species

The domestication and improvement of fruit-bearing crops resulted in a large diversity of fruit form. To facilitate consistent terminology pertaining to shape, a controlled vocabulary focusing specifically on fruit shape traits was developed. Mathematical equations were established for the attributes so that objective, quantitative measurements of fruit shape could be conducted. The controlled vocabulary and equations were integrated into a newly developed software application, Tomato Analyzer, which conducts semiautomatic phenotypic measurements. To demonstrate the utility of Tomato Analyzer in the detection of shape variation, fruit from two F2 populations of tomato (Solanum spp.) were analyzed. Principal components analysis was used to identify the traits that best described shape variation within as well as between the two populations. The three principal components were analyzed as traits, and several significant quantitative trait loci (QTL) were identified in both populations. The usefulness and flexibility of the software was further demonstrated by analyzing the distal fruit end angle of fruit at various user-defined settings. Results of the QTL analyses indicated that significance levels of detected QTL were greatly improved by selecting the setting that maximized phenotypic variation in a given population. Tomato Analyzer was also applied to conduct phenotypic analyses of fruit from several other species, demonstrating that many of the algorithms developed for tomato could be readily applied to other plants. The controlled vocabulary, algorithms, and software application presented herein will provide plant scientists with novel tools to consistently, accurately, and efficiently describe two-dimensional fruit shapes.