Peach is an economically important fruit tree crop worldwide. The external color of fruit impairs peach price, especially fruits with different degrees blush. Developing varied skin color cultivars by molecular breeding is expected to satisfy the market demands for diverse peach fruits. Although, the variations in key genes regarding whether the skin is colored have been found, their markers have not really been widely used in the breeding process, and the molecular marker development of peach skin blush awaits promotion and application. The goal of this study was to explore the variations related to peach skin color, and to develop molecular markers for breeding based on variations. By analyzing the expression of anthocyanin synthesis-related and regulatory genes, we confirmed that the MYB10.1 is a key gene control skin color. We further found that 5243 bp insertion and 483 bp deletion in MYB10.1 promoter were closely related to peach skin color phenotype. In addition, we identified one transposon insertion mutation at the − 2706 bp position of MYB10.1 promoter related to non-red fruit skin trait and developed a marker for validation. The size of the insertion amplified from the ShiYuBaiTao genome DNA was approximately 3.5 kb. However, it does not completely explain the phenomenon of non-red skin of peach just as MYB10.1-2/MYB10.1-2 and accuracy were 36.1% in this study. Based on the results of this work, we propose that MYB10.1-2/MYB10.1-2 should not only be a genotype of non-red skin, but also should be combined with other makers to predict the color of peach skin color.

Jujube (Ziziphus jujuba Mill.) is a fruit tree that is gaining increasing importance in drought-affected regions worldwide. The fruit size is an important quantitative agronomic trait that affects not only the fruit yield and attractiveness but also consumer preference. Genetic enhancement of fruit appearance is a fundamental goal of jujube breeding programs. The genetic control of jujube fruit size traits is highly quantitative, and development of high-density genetic maps can facilitate fine mapping of quantitative trait loci (QTLs) and gene identification. However, studies regarding the construction of high-density molecular linkage maps and identification of quantitative trait loci (QTLs) targeting fruit size in jujube are limited. In this study, we performed whole-genome resequencing of the jujube cultivars “JMS2” and “Xing16” and their 165 F1 progenies to identify genome-wide single-nucleotide polymorphism (SNP) markers and constructed a high-density bin map of jujube that can be used to assist in the selection of multiple traits in jujube breeding. This analysis yielded a total of 116,312 SNPs and a genetic bin map of 2398 bin markers spanning 1074.33 cM with an average adjacent interval of 0.45 cM. A quantitative genetic analysis identified 15 QTLs related to fruit size and the observed phenotypic variation associated with a single QTL ranged from 9.5 to 13.3%. Through the screening of overlapping and stable QTL regions, we identified 113 candidate genes related to fruit size. These genes were ascertained to be involved in cell division, cell wall metabolism, synthesis of phytohormones (ABA, IAA, and auxin), and encoding of enzymes and transcription factors. These candidate genomic regions will facilitate marker-assisted breeding of fruits with different sizes and shapes and lay a foundation for future breeding and manipulation of fruit size and shape in jujube.

Peach is an economically important fruit tree crop worldwide. The external color of the fruit governs the peach price, especially in fruits with different degrees of blush. Molecular marker-assisted breeding has become a necessary part of modern breeding practices, increasing their efficiency. Although the key related genes responsible for peel coloration have been found in peach, corresponding molecular markers have not been widely used in peach breeding. The development of molecular markers for peach peel color needs to be advanced and implemented in practice. This study aimed to explore the variation related to peach skin color and to develop molecular markers linked to these variants that can be used in breeding. By analyzing the expression of anthocyanin synthesis-related and regulatory genes, we confirmed that MYB10.1 is a key gene controlling skin color. We further identified that 5243 bp insertion and 483 bp deletion in the MYB10.1 promoter was highly associated with peach skin color phenotypes. In addition, we identified one transposon insertion mutation at the −2706 bp position of the MYB10.1 promoter associated with the non-red fruit skin trait and developed a molecular marker for validation. The insertion size amplified from the ‘ShiYuBaiTao’ genome DNA was approximately 3.5 kb. However, it explained a lower percentage of the non-red skin phenotype variance in peach, at 36.1%, compared to MYB10.1-2/MYB10.1-2 in this study. Based on these results, we propose that MYB10.1-2/MYB10.1-2 should not only be the only non-red skin genotype assessed but should also be combined with other molecular makers to increase the prediction accuracy of peach skin color.