Fig 2 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
![Regions identified by GWA in eggplant LG E01-E06 in comparison to QTL locations described by Portis et al. [2].
The GWA outcome is given to the left of each chromosome (the vertical bars represent a ±3.4 cM interval around the position of the associated SNP loci) and the various regions are marked in red. The QTL locations are shown to the right of each chromosome.](profile/Fabio-Cericola-2/publication/281610817/figure/fig5/AS:339879176228898@1458044918888/Regions-identified-by-GWA-in-eggplant-LG-E01-E06-in-comparison-to-QTL-locations-described.png)
Regions identified by GWA in eggplant LG E01-E06 in comparison to QTL locations described by Portis et al. [2]. The GWA outcome is given to the left of each chromosome (the vertical bars represent a ±3.4 cM interval around the position of the associated SNP loci) and the various regions are marked in red. The QTL locations are shown to the right of each chromosome.
Source publication
An eggplant ( Solanum melongena ) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which ta...
Similar publications
In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms...
The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored.
We investigated genotypic variation in the production of SET and its relationship with...
The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticist and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the 6-...
Citations
... The quality of vegetables is defined both by external attributes, such as color, shape, size and freshness, as well as internal characteristics such as firmness, flavor, mineral content, health-promoting compounds and sensory parameters. In particular, the evaluation of fruit firmness is important both for the organoleptic characteristics and shelf life of eggplant fruits [45], and it can be influenced by several factors, including soil nitrogen availability. Radicetti et al. [46] noted that, when eggplant cultivation is preceded by a legume crop, fruit firmness is greater compared to firmness levels recorded when preceded by grasses and brassicas. ...
Low-density polyethylene (LDPE) mulching films have an important function in crop cultivation; at the end of their life, however, their removal and disposal become both an economic and environmental problem. One possible alternative to low-density polyethylene (LDPE) mulch is provided by certified soil-biodegradable mulch films, such as those produced by Novamont and commercially available under the trade name MaterBi ®. MaterBi is a biodegradable thermoplastic material made with starch and a biodegradable copolyester based on proprietary technology. In this study, we compared two biodegradable MaterBi ®-based films (commercial and experimental films) with bare soil and a low-density polyethylene to evaluate their effect on yield and on a number of qualitative characteristics (organoleptic and nutraceutical composition) of eggplant fruits (cv Mirabelle F1) grown in two different regions in Southern Italy (Sicily and Campania). In our study, the use of biodegradable MaterBi ® films improved not only yield and production parameters, such as the number and average weight of fruits, but also lipophilic and hydrophilic antioxidant activity and phenolic and ascorbic acid content. For many parameters, responses differed according to the cultivation environment and, in particular, the site's pedoclimatic conditions. Our results suggest that biodegradable MaterBi ®-based mulching films are a potentially valid alternative to traditional LDPEs, providing the production and quality benefits reported above and promoting environmental sustainability, thanks to their positive biodegradable properties.
... Phenotype and genotype associations were detected for 30 of the 33 traits. An association map was constructed with 79 SNP marker loci in 39 distinct chromosomal regions distributed on all chromosomes (Portis et al., 2015). Salgon et al. (2018) developed a mapping population from intraspecific cross-sections of MM738 (susceptible) × EG203 (resistant) to identify QTLs resistant to Ralstonia solanacearum strains in Brinjal. ...
Brinjal, eggplant or aubergine (Solanum melongena L.) belongs to the Solanaceae family and is a widely cultivated warm-season vegetable in India and around the world. Brinjal production and productivity are strongly affected by many biotic stresses, viz., fusarium wilt, verticillium wilt and small leaves of brinjal. Among all the diseases, bacterial wilt (BW) is the most destructive disease in tropical, subtropical, temperate, and humid regions worldwide due to the broad host range and prolonged duration of spore survival. BW disease in brinjal is caused by Ralstonia solanacearum, which belongs to the β-proteobacteria family and is a gram-negative, nonspore-forming, rod-shaped, and soilborne bacterium. BW disease management strategies, such as culture, mechanical, biological, and chemical methods, are ineffective due to the prolonged survival period of the bacterium in the soil and its wide host range. The use of resistant varieties and hybrids against BW disease is the safest method for controlling this disease. Information on the genetics of resistance to BW disease in brinjal is vital for the development of an effective breeding method and for identifying bacterial wilt resistance in preferable brinjal cultivars. The use of molecular markers associated with BW disease resistance gene loci helps to characterize traits of interest and develop resistant varieties and hybrids. This review described recent advances in different control measures. We focused on the importance of marker-assisted selection for identifying bacterial wilt diseases.
... The 194 both phenotype and genotype associations were discovered, related to 30 of the 33 measured traits. The association of 79 SNP marker loci was mapped to 39 distinct chromosomal regions and distributed all 12 brinjal chromosomes [21,22]. identified the QTLs resistant to Ralstonia solanacearum strains in brinjal mapping population derived from intraspecific cross between MM738 (susceptible) × EG203 (resistant). ...
Brinjal is a warm–season vegetable that belongs to the Solanaceae family. Among the biotic stresses of brinjal, bacterial wilt is a major disease caused by a soil-borne bacterium, Ralstonia solanacearum. Both cultural and chemical disease control methods are not effective due to the wide host range and prolonged spore survival periods in soil. In recent past, the use of resistant varieties and hybrids are recognized as the effective method to control bacterial wilt disease. Information on genetics of resistance to bacterial wilt disease is of prime importance for improvement of varieties and hybrids in brinjal. The bacterial wilt resistance response and resistance mechanisms are strictly based on the environmental conditions and cultivars. In traditional crop improvement methods, the development of varieties and hybrids is expensive and time consuming. The discovery of molecular marker systems increases the speed and precision for developing of varieties and hybrids with desired agronomic traits.
... Phenotyping of eggplant wild relatives. Phenotyping using morphological descriptors is crucial for the preliminary identification and selection of genotypes for breeding and crop improvement 31 . In the present study, thirteen diverse eggplant species were phenotypically discriminated using the forty morphological descriptors illustrating a close relationship among the eggplant wild relatives. ...
Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic
discriminations among 13 eggplant species deploying chloroplast–plastid (Kim matK) and nuclear (ITS2) short gene sequences (400–800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99–100%) than in the ITS2 region (80–90%). The eggplant species showed 13 unique secondary structures with a central ring
with various helical orientations. Principal component analysis (PCoA) provides the descriptor–wise phenotypic clustering, which is essential for trait–specifc breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants.
... The diversity present within the cultivated eggplant is of great interest for eggplant breeding and has allowed the development of significantly improved modern cultivars (Daunay and Hazra, 2012). However, as occurs with many other vegetables, this high morphological diversity is mostly the consequence of genetic variation in a few major genes, particularly those related to fruit traits (Daunay et al., 2004;Portis et al., 2015;Mangino et al., 2021;Arrones et al., 2022;Guan et al., 2022), and the overall genetic variation of the crop is narrow (Acquadro et al., 2017;Barchi et al., 2019a;Liu et al., 2019). Therefore, the exploitation of the genetic diversity present in other cultivated eggplants (S. aethiopicum and S. macrocarpon) and wild relatives represents a promising avenue for developing improved eggplant materials by incorporating their unique traits (Oyelana and Ugborogho, 2008;Prohens et al., 2012;. ...
... Eggplant displays a large diversity of fruit sizes, shapes, and colors, facilitating breeding for outer fruit quality and appearance traits. Quantitative trait loci (QTL) have been identified for fruit morphological traits (Portis et al., 2015;Toppino et al., , 2020Barchi et al., 2019c;Mangino et al., 2021), although few causative genes have been identified. One exception is the APRR2 gene (Arrones et al., 2022), which controls the synthesis of fruit peel chlorophyll, as well as several genes involved in anthocyanin synthesis (Florio et al., 2021;He et al., 2022;Li et al., 2022). ...
... Subsequently, a selected eggplant association panel of 191 selected accessions (Cericola et al., 2013), comprising a mixture of breeding lines, old varieties, and landrace selections originating from Asia and the Mediterranean Basin, was genotyped and phenotyped. This allowed the identification and positioning of several marker/ trait associations related to fruit, plant, and leaf morphological traits relevant to eggplant breeding (Cericola et al., 2014;Portis et al., 2015) as well as the identification of contrasting genotypes for nitrogen use efficiency (Mauceri et al., 2020) and, most recently, identification of the gene networks responsible of such diversity (Mauceri et al., 2021). Subsequently, Miyatake et al. (2019) genotyped 893 accessions, mostly from Asia, with 831 SNP and 50 SSR markers and established a core collection of 100 accessions (World Eggplant Core; WEC). ...
Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. Eggplant is closely related to over 500 species of Solanum subgenus Leptostemonum, belonging to its primary, secondary, and tertiary genepools, and exhibits a wide range of characteristics, including adaptive traits to climate change, that are useful for eggplant breeding. Germplasm banks worldwide hold more than 19,000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in eggplant relatives can greatly contribute to a revolution in eggplant breeding. The recent creation of new genetic resources, such as mutant libraries, core collections, recombinant inbred lines (RILs), and sets of introgression lines (ILs) will be another crucial element for an eggplant breeding revolution, which will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.
... A first attempt was conducted by Ge et al. [60] to identify functional genes and QTLs related to fruit-related traits using a panel of 141 eggplant accessions. Afterwards, a larger panel (191 accessions) was employed to analyze the marker/trait associations for key breeding fruit and plant traits [61][62][63]. The described association mapping studies not only highlighted numerous previously identified genes/QTLs, but also allowed the discovery of novel loci and candidate genes, providing a valuable resource for the development of a marker-assisted selection breeding strategy. ...
... Many eggplant cultivars present prickles on the fruit calyx, since in certain world regions they are perceived of superior organoleptic quality, while the prickles on the vegetative tissues are generally absent, as the result of the positive selection in breeding programs [79]. Despite the several mapping studies that reported QTLs for this trait [24,27,42,62,63,80], the genetic basis of prickle formation in eggplant remains unclear. Data collection revealed a total of 115 QTLs and, on comparing these regions, 20 unique QGRs were defined (Table S2; Figure 2). ...
... prickles on the fruit calyx, since in certain world regions they are perceived of superior organoleptic quality, while the prickles on the vegetative tissues are generally absent, as the result of the positive selection in breeding programs [79]. Despite the several mapping studies that reported QTLs for this trait [24,27,42,62,63,80], the genetic basis of prickle formation in eggplant remains unclear. Data collection revealed a total of 115 QTLs and, on comparing these regions, 20 unique QGRs were defined (Table S2; Figure 2). ...
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant’s traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
... Parameters such as plant height, plant growth type, leaf size, number of flowers, flower size, flower color are the basic parameters in breeding and are also related to fruit size, fruit color and yield. Some researchers reported that flower size (Genç, 2014), flower color, flower location (Kowalska, 2008), the number of flowers per flowering (Portis et al., 2015) was related to fruit size, fruit color and number of fruits. On the other hand, some researchers noted that plant height (Miceli et al., 2014), leaf size, leaf formation, growth habit (Portis et al., 2015) are associated with strong growth, high yield and ease of harvest. ...
... Some researchers reported that flower size (Genç, 2014), flower color, flower location (Kowalska, 2008), the number of flowers per flowering (Portis et al., 2015) was related to fruit size, fruit color and number of fruits. On the other hand, some researchers noted that plant height (Miceli et al., 2014), leaf size, leaf formation, growth habit (Portis et al., 2015) are associated with strong growth, high yield and ease of harvest. Eggplant morphological descriptors, which are highly effective in eggplant, are used to reveal the differences caused by grafting . ...
... Breeders are working on the development of new rootstocks that can contribute to the growth habit of eggplant scion (Boyaci & Ellialtioglu, 2020). Portis et al., (2015) noted that is important for the upright habit of the plant. Furthermore Quamruzzaman et al., (2020) reported that a compatible rootstock / scion combination might cause less damage to the plant and fruit in cultural processes. ...
... To dissect this important trait for eggplant genetics and breeding, in this study we have combined classical forward genetics techniques with advanced association and sequencing analyses, using both experimental populations and germplasm materials to identify and validate a candidate gene controlling the synthesis of fruit peel chlorophyll. Up to now, the dissection of complex traits in eggplant has been usually performed using germplasm panels (Portis et al., 2015) or temporary mapping populations, such as F 2 and BC 1 (Barchi et al., 2012;Miyatake et al., 2016;Pandiyaraj et al., 2019;Bhanushree et al., 2020). These populations have the advantage of being easy and fast to develop but are not as powerful as the immortal ones to identify strong associations, candidate genes or causative SNPs, and accumulate fewer genetic recombination events, limiting the resolution for QTL detection (Arrones et al., 2020). ...
Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.
... Studying and understanding the association of agro-morphological trait variations with genetic variable sites may assist in the selection and transformation of desirable traits to develop new cultivars through breeding programs. Diverse agro-morphological variations (fruit and leaf) of eggplant germplasm were found in previous studies [35][36][37]. Similarly, in this study, eggplant genetic resources collected from different countries possessed diverse agro-morphological characteristics. ...
... Genome-wide association studies have proved its efficiency in finding genomic regions linked with economically important agronomical features in several crops, including wheat [39][40][41][42], eggplant [36], potato [43], and soybean [44,45]. There are important agro-morphological traits to be improved in eggplant, including the development of prickleless varieties. ...
Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desirable traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and ge-nome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.
... Interestingly, these correlations were not N-treatment dependent. The same happened among traits related to fruit morphology, also in agreement with several studies (Portis et al., 2015;Mangino et al., 2021). ...
Lowering nitrogen inputs is a major goal for sustainable agriculture. In the present study, a set of 10 Solanum melongena introgression lines (ILs) developed using S. incanum as the exotic donor parent were grown under two nitrogen fertilization doses supplied with the irrigation system: 1) 8.25 mmol · L⁻¹ NH4NO3, corresponding to the high nitrogen treatment (HN), and 2) no external nitrogen supply, corresponding to the low nitrogen treatment (LN). Twenty traits, including plant growth and yield parameters, fruit size and morphology, nitrogen and carbon content in leaf and fruit, and phenolics content in fruit, were evaluated. The aim was to select of potential materials for eggplant breeding under low N inputs, as well as to identify and locate putative QTLs associated with the traits evaluated. No significant differences were observed between the soil characteristics of the HN and LN treatments, except for nitrogen and iron content, which was slightly lower in the HN, probably as a consequence of higher nutrient removal from soil by plants in the latter group. Analysis of variance showed that lowering nitrogen inputs did not significantly affect the final yield, fruit morphology, size and phenolics content. Most agronomic traits were highly and positively correlated with each other under both treatments, as well as total phenolics with chlorogenic acid content. The assessment of the differences between each IL and the recipient parent resulted in the identification of 36 QTLs associated with most of the traits—12 were specific to the HN, 17 specific to the LN, and 7 were stable across treatments. The introgressed fragment of S. incanum generally had a negative effect on the trait, except for QTLs for fruit dry matter, for fruit length on chromosome 10 under the HN, and for fruit pedicel length on chromosome 9 under the LN. The increase over AN-S-26 of the allele of S. incanum for the QTLs detected ranged between –73.98% and 26.03% in HN and –73.67% and 34.43% in LN. These findings provide useful tools for the utilization of S. incanum in eggplant breeding under lower nitrogen fertilization.
