Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant

Abstract

Eggplant (Solanum melongena; 2n = 24) is an economically important fruit crop of the family Solanaceae that was domesticated in India and Southeast Asia. Construction of a high-resolution genetic map and map-based gene mining in eggplant have lagged behind other crops within the family such as tomato and potato. In this study, we conducted high-throughput single nucleotide polymorphism (SNP) discovery in the eggplant genome using specific length amplified fragment (SLAF) sequencing and constructed a high-density genetic map for the quantitative trait locus (QTL) analysis of multiple traits. An interspecific F 2 population of 121 individuals was developed from the cross between cultivated eggplant "1836" and the wild relative S. linnaeanum "1809." Genomic DNA extracted from parental lines and the F 2 population was subjected to high-throughput SLAF sequencing. A total of 111.74 Gb of data and 487.53 million pair-end reads were generated. A high-resolution genetic map containing 2,122 SNP markers and 12 linkage groups was developed for eggplant, which spanned 1530.75 cM, with an average distance of 0.72 cM between adjacent markers. A total of 19 QTLs were detected for stem height and fruit and leaf morphology traits of eggplant, explaining 4.08-55.23% of the phenotypic variance. These QTLs were distributed on nine linkage groups (LGs), but not on LG2, 4, and 9. The number of SNPs ranged from 2 to 11 within each QTL, and the genetic interval varied from 0.15 to 10.53 cM. Overall, the results establish a foundation for the fine mapping of complex QTLs, candidate gene identification, and marker-assisted selection of favorable alleles in eggplant breeding.

A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

“…Gene prediction was conducted by homology comparison based on the syntenic relationship between eggplant and tomato, which yielded 11 homologous genes for fruit size on eggplant chromosome E03. Combining these results with the identification of the QTL region FS3.1 in our previous study 30 , we propose that Smechr0301963 (the ortholog from S. melongena-67/3 is SMEL_003g182360), a gene potentially orthologous to SUN gene family members, is a key candidate gene for regulating eggplant fruit length.…”

“…Our study provides a high-quality eggplant genome that has wide applications in eggplant genetics and genomics studies, such as marker development, gene detection and chromosome evolution. In the present study, we detected QTL hotspots based on published QTL mapping results and marker information [23][24][25][26][27][28][29][30] , with 210 markers associated with 71 traits anchored to the S. melongena-HQ reference genome ( Fig. 8; Supplementary Table S10).…”

“…The average length (L), diameter (D), and fruit shape index (L/D) of three fruits from each F 2 individual were measured to determine the value for the individual plant ( Supplementary Table S9). Based on genotyping Based on the QTL results of previous studies and the available marker sequence information, we anchored these markers to our latest reference genome to investigate QTL hotspots in eggplant [23][24][25][26][27][28][29][30] . A total of 210 linkage markers related to 71 traits, including fruit-related traits (i.e., fruit size and color), leaf morphology, and nutrient components, were anchored (Fig.…”

A New Intra-Specific and High-Resolution Genetic Map of Eggplant Based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour

“…Despite recent efforts, the linkage maps used for identifying the genetic basis of traits of breeding interest are still not saturated, hampering the fine mapping of QTL regions and the identification of candidate genes associated with the phenotypic traits. Up to now, the only available high-resolution SNP-based linkage map was developed on a F 2 population from the inter-specific cross (S. melongena × S. linneanum) and was employed to highlight QTLs affecting stem height and fruit and leaf morphology [35].…”

Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

“…Importantly, QTLs linked to net photosynthetic rate (P N ) and stomatal conductance proposed critical for the plant growth and development of goji berry [24]. SLAF-seq, a high throughput reduced representation sequencing strategy for large scale SNP discovery has been practiced due to numerous advantages [34][35][36][37][38], in different crop plants including pepper [29], maize [30], walnut [31], cauli ower [32], eggplant [55], and Salvia miltiorrhiza [33]. Moreover, SLAF-seq is widely applied to different woody perennial tree plants and e ciently generated genetic maps based on F 1 population [25-35-24].…”