Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis

Zongwei Qian; Yanhai Ji; Ranhong Li; Sergio Lanteri; Haili Chen; Longfei Li; Zhiyang Jia; Yanling Cui

doi:10.3389/fgene.2022.841198

Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis

Front Genet. 2022 May 18:13:841198. doi: 10.3389/fgene.2022.841198. eCollection 2022.

Authors

Zongwei Qian^{1

2

3}, Yanhai Ji^{1

2

3}, Ranhong Li⁴, Sergio Lanteri⁵, Haili Chen^{1

2

3}, Longfei Li⁶, Zhiyang Jia⁶, Yanling Cui^{1

2

3}

Affiliations

¹ National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
² Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China.
³ Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China.
⁴ College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China.
⁵ DISAFA, Plant Genetics and Breeding, University of Turin, Grugliasco, Italy.
⁶ Jingyan Yinong (Beijing) Seed Sci-Tech Co. Ltd., Beijing, China.

Abstract

Eggplant (Solanum melongena L.; 2n = 24) is one of the most important Solanaceae vegetables and is primarily cultivated in China (approximately 42% of world production) and India (approximately 39%). Thousand-grain weight (TGW) is an important trait that affects eggplant breeding cost and variety promotion. This trait is controlled by quantitative trait loci (QTLs); however, no quantitative trait loci (QTL) has been reported for TGW in eggplant so far, and its potential genetic basis remain unclear. In this study, two eggplant lines, 17C01 (P1, wild resource, small seed) and 17C02 (P2, cultivar, large seed), were crossed to develop F1, F2 (308 lines), BC1P1 (44 lines), and BC1P2 (44 lines) populations for quantitative trait association analysis. The TGWs of P1, P2 and F1 were determined as 3.00, 3.98 and 3.77 g, respectively. The PG-ADI (polygene-controlled additive-dominance-epistasis) genetic model was identified as the optimal model for TGW and the polygene heritability value in the F2 generation was as high as 80.87%. A high-quality genetic linkage bin map was constructed with resequencing analysis. The map contained 3,918 recombination bins on 12 chromosomes, and the total length was 1,384.62 cM. A major QTL (named as TGW9.1) located on chromosome 9 was identified to be strongly associated with eggplant TGW, with a phenotypic variance explanation of 20.51%. A total of 45 annotated genes were identified in the genetic region of TGW9.1. Based on the annotation of Eggplant genome V3 and orthologous genes in Arabidopsis thaliana, one candidate gene SMEL_009g329850 (SmGTS1, encoding a putative ubiquitin ligase) contains 4 SNPs and 2 Indels consecutive intron mutations in the flank of the same exon in P1. SmGTS1 displayed significantly higher expression in P1 and was selected as a potential candidate gene controlling TGW in eggplant. The present results contribute to shed light on the genetic basis of the traits exploitable in future eggplant marker-assisted selection (MAS) breeding.

Keywords: PG-ADI models; QTLs; eggplant; thousand-grain weight (TGW); ubiquitin-proteasome pathway.