Study on the strategy for genotype identification of fruit weight traits to assist breeding in peach

【Objective】The fruit weight of peaches is a quantitative trait influenced by multiple genes. This paper provides a comprehensive summary of the molecular markers associated with fruit weight, which have been identified in previous studies. It also evaluates the breeding value of fruit weight in cultivated varieties in China, focusing exclusively on the additive effects between loci. Furthermore, this study identifies and recommends parental materials that can be utilized to improve existing varieties.【Methods】Building on both domestic and international research advancements, this study synthesized the molecular markers associated with fruit weight as identified by previous researchers. Utilizing the 574 genome resequencing data generated by our team, we employed Trimmomatic software to ensure the quality control of the raw sequencing data, resulting in filtered sequences. Subsequently, BWA software facilitated sequence alignment, while GATK software was employed for variant detection, ultimately enabling the determination of each variety's genotype. Genotypic effect values were calculated as follows: the allelic effects of SNP loci on traits were estimated by comparing the phenotypic values of different genotypes [homozygous reference (0/0), heterozygous (0/1), and homozygous mutant (1/1)] in pairs. Alleles were classified as positive if there was a significant increase in phenotypic values between the homozygous reference and other genotypes; otherwise, they were classified as negative. Additionally, we screened and recommended parental materials for the improvement of current varieties by incorporating locus effect values.【Results】Drawing upon research advancements both domestically and internationally, this study identified markers with specific chromosomal locations, including SNPs and Indels, ultimately selecting 46 markers from eight research teams. An analysis of marker positions revealed that the numbers of markers on chromosomes 1 through 8 were 5, 6, 4, 9, 3, 12, 2, and 5, respectively, indicating a higher concentration of loci on chromosomes 4 and 6. Utilizing genetic variation data from 574 peach cultivars collected in the initial phase of laboratory research, the linkage disequilibrium (LD) of the germplasm was calculated. The physical distance at which the LD intensity (r 2 ) decayed to a standard level was used as the threshold for merging loci, resulting in a reduction of loci to 25. Additionally, 19 marker sites were identified after excluding 6 markers that were significantly divergent from the germplasm. These loci can be utilized to assess their contribution to the trait of fruit weight in natural populations, with the effect values of these 19 loci exhibiting significant heterogeneity. Among these, three loci (N3, N10, and N19) exhibited strong positive effects, with the N3 locus at the terminus of chromosome 1 showing the highest effect value of 10.86. Conversely, five loci (N11, N13, N15, N16, and N17) demonstrated strong negative effects, with the N15 locus at the apex of chromosome 6 having the lowest effect value of -20.06. Neutral effect sites, with values ranging from -1.72 to 1.04, constituted 36.84% of the total. With three superior varieties (Zhongyoupan 7, Zhongyoupan 15, and Huaguang), the breeding values of the parents of Zhongyoupan 7 and Zhongyoupan 15 exhibited minor fluctuations throughout the breeding process; however, the overall trajectory was upward. In contrast, during the breeding of Huaguang, the breeding value for fruit weight showed a linear decline, aligning with the downward trend observed in the actual fruit weight phenotype during the breeding process. Furthermore, an analysis of the 30 principal varieties currently under cultivation revealed a highly significant positive correlation between the predicted effect values and the actual observed values, with an R2 of 0.467 3 (r0.01,28 = 0.462 8, P = 3.125 0E-05). Among these 30 main varieties, 24 exhibited negative effects at the N15 locus, which had the highest effect value, and 19 exhibited negative effects at the N13 locus, which had the second highest effect value. Consequently, all these varieties can be hybridized with germplasm (including wild germplasm, local varieties, or other breeding varieties) possessing the mutation site, and the molecular marker-assisted selection can be conducted through genotype identification. Utilizing the identified markers, the parent germplasm with significant improvement potential for key cultivated varieties, such as Changling Zaoyulu, Jinlin 8903, Wanpantao, Jietubai and Baihua, was selected from local varieties.【Conclusion】In conclusion, this study identified and screened 19 markers associated with fruit weight, and their effect values were aggregated. The breeding values of the parent materials and 30 primary varieties were calculated during the cross-breeding process of three different varieties. The results demonstrated a correlation between the breeding values and the observed phenotype of fruit weight, thereby confirming that these markers are applicable in molecular- assisted breeding for enhancing fruit weight, which realized the early prediction of fruit weight phenotype of peach.