Dissection of the Pearl of Csaba pedigree identifies key genomic segments related to early ripening in grape

Abstract

Pearl of Csaba (PC) is a valuable backbone parent for early-ripening grapevine (Vitis vinifera) breeding, from which many excellent early ripening varieties have been bred. However, the genetic basis of the stable inheritance of its early ripening trait remains largely unknown. Here, the pedigree, consisting of 40 varieties derived from PC, was re-sequenced for an average depth of ∼30×. Combined with the resequencing data of 24 other late-ripening varieties, 5,795,881 high-quality single nucleotide polymorphisms (SNPs) were identified following a strict filtering pipeline. The population genetic analysis showed that these varieties could be distinguished clearly, and the pedigree was characterized by lower nucleotide diversity and stronger linkage disequilibrium than the non-pedigree varieties. The conserved haplotypes (CHs) transmitted in the pedigree were obtained via identity-by-descent analysis. Subsequently, the key genomic segments were identified based on the combination analysis of haplotypes, selective signatures, known ripening-related quantitative trait loci (QTLs), and transcriptomic data. The results demonstrated that varieties with a superior haplotype, H1, significantly (one-way ANOVA, P < 0.001) exhibited early grapevine berry development. Further analyses indicated that H1 encompassed VIT_16s0039g00720 encoding a folate/biopterin transporter protein (VvFBT) with a missense mutation. VvFBT was specifically and highly expressed during grapevine berry development, particularly at veraison. Exogenous folate treatment advanced the veraison of "Kyoho". This work uncovered core haplotypes and genomic segments related to the early ripening trait of PC and provided an important reference for the molecular breeding of early-ripening grapevine varieties.

Figure 1

The four-generation pedigree chart of the “Pearl of Csaba”. The circle, box, and text with background color indicate the founder, descendants, and hybrid parents in pedigree, respectively. Different berry ripening traits are represented by different colors, and varieties with character background colors are sequenced in this study.

Figure 2

Population structure of early-pedigree and late-cultivar samples. A, PCA plot among all varieties of early-pedigree (red) and late-cultivar (blue). B, Unrooted NJ tree across all samples, the unit of tree scale is P distance. C, Genome-wide averaged distance of LD decayed to r² = 0.2 for the groups of early-pedigree (red), late-cultivar (blue), and all varieties (black). Comparison of levels of D, heterozygosity, E, nucleotide diversity, and F, Hardy–Weinberg equilibrium between the early-pedigree and the late-cultivar. The elements of boxplot are the center line, median; box limits, upper and lower quartiles; whiskers, 1.5 × interquartile range; points, outliers. In heterozygosity, the four outliers in the early group are “Feicui Rose”, “Wuhezaohong”, “Hongbiaowuhe”, and “Chunguang” from low to high; similarly, the five outliers in the late group are “Neijingxiang”, “Tamnara”, “Tano Red”, “Miguang”, and “Catawba”. All outliers belong to Vitis vinifera × Vitis labrusca.

Figure 3

Transmission pattern of CHs in the “Pearl of Csaba” breeding. The top is the distribution of homozygous haplotypes on chromosomes in the “Pearl of Csaba” and from the top to the bottom is the flow of the pedigree. Different colors represent different generations: F1 (red), F2 (blue), F3 (yellow), and F4 (green). A shadow and asterisks mark chr16 positions of interest (i.e. shown in Figure 5A). The transmission pattern of chromosome 16 is shown.

Figure 4

The identification procedure of candidate genes related to the early-ripening trait. A, Distribution of CHs on 19 chromosomes. The genome-wide selective sweeps detected by B, π_late/π_early, C, Fixation index (F_ST), and D, Cross-population composite likelihood ratio test (XP-CLR). E, Genome-wide distribution of QTL for flowering, veraison, and ripening in grapevine. The “*” indicates the genomic region under selection where the 47 candidate genes are located. F, The gene name or id of 47 candidate genes related to early-ripening trait, and G, their log₂FC value in “Xiangfei” (X) and “Zaomeiguixiang” (Z) compared with “Italia” at three berry developmental stages, and H, the number and distribution of their fixed SNPs (Fisher-exact P-value < 0.0001).

Figure 5

A superior haplotype is associated with the early-ripening trait in the pedigree. A, Two selective signatures, F_ST: fixation index (black line) and XP-CLR: Cross-population composite likelihood ratio test (red line), were detected simultaneously in the gray shade (chr16: 353.37- 365.97 kb) of a long haplotype carrying multiple genes. The black dashed line and the red dashed line indicate the top 5% values of F_ST and XP-CLR, respectively. B, The two genes contained in the gray shade and their six haplotypes consisting of 14 SNPs associated with VvFBT inferred from 80 varieties (32 early ripening and 48 late-ripening varieties). C, Box plot of berry development period (BDP; in days) for the genotype of 80 varieties carrying H1–H6 haplotypes. The significant difference between test methods and post hoc tests are one-way ANOVA (P < 0.001) and LSD, respectively. D, The number and proportion of genotype of a missense SNP (chr16:360203) located on VvFBT, and number and proportion of H1–H6 haplotypes in early-ripening, late-ripening, and wild grapevine groups. E, The phenotype of control, and exogenous 0.1 mmol•L⁻¹, 0.5 mmol•L⁻¹ and 1 mmol•L⁻¹ folate treatment (y axis) of “Kyoho” at different development stages (x axis). A row represents the variation of the same bunch of “Kyoho” at 35, 55, 67, 72, and 79 days after flowering (DAF; in x axis). Images have been digitally extracted for comparison.