Genetic and phenotypic analyses reveal major quantitative loci associated to fruit size and shape traits in a non-flat peach collection (P. persica L. Batsch)

Comprehensive analysis of transcriptome and metabolome identified the key gene networks regulating fruit length in melon

BACKGROUND

Melon is an ideal crop model for studying fruit development. Fruit shape is an important quality trait, and fruit length is a key indicator affecting fruit shape. However, studies on the genes regulating melon fruit length are still limited.

RESULTS

In this study, we investigated the gene network regulating fruit morphology in melons utilizing transcriptome profile and a co-expression pattern-based approach. Four co-expression modules/gene networks highly correlated with changes in endogenous plant hormone levels at different developmental stages were identified. We pinpointed 11 key genes associated with cell development, 4 genes related to microtubule development, and 16 genes involved in the auxin (IAA, indole-3-acetic acid) pathway. These genes were identified as module hubs, and their expression level correlated with phenotypic variation. Through rigorous screening methods, we enhanced the likelihood that these genes are genuine candidates in the regulation of the fruit morphology network. These genes play a significant role in controlling fruit length, providing crucial insights into the molecular mechanisms underlying melon fruit development.

CONCLUSIONS

Our findings revealed candidate genes that regulate melon fruit length, helping in the understanding of the molecular mechanisms underlying melon fruit development. These genes will be valuable for implementing marker-assisted breeding strategies.

Using Quantitative Trait Locus Mapping and Genomic Resources to Improve Breeding Precision in Peaches: Current Insights and Future Prospects

Modern breeding technologies and the development of quantitative trait locus (QTL) mapping have brought about a new era in peach breeding. This study examines the complex genetic structure that underlies the morphology of peach fruits, paying special attention to the interaction between genome editing, genomic selection, and marker-assisted selection. Breeders now have access to precise tools that enhance crop resilience, productivity, and quality, facilitated by QTL mapping, which has significantly advanced our understanding of the genetic determinants underlying essential traits such as fruit shape, size, and firmness. New technologies like CRISPR/Cas9 and genomic selection enable the development of cultivars that can withstand climate change and satisfy consumer demands with unprecedented precision in trait modification. Genotype-environment interactions remain a critical challenge for modern breeding efforts, which can be addressed through high-throughput phenotyping and multi-environment trials. This work shows how combining genome-wide association studies and machine learning can improve the synthesis of multi-omics data and result in faster breeding cycles while preserving genetic diversity. This study outlines a roadmap that prioritizes the development of superior cultivars utilizing cutting-edge methods and technologies in order to address evolving agricultural and environmental challenges.

Multiple Localization Analysis of the Major QTL-sfw 2.2 for Controlling Single Fruit Weight Traits in Melon Based on SLAF Sequencing

Cucumis melo is an annual dicotyledonous trailing herb. It is fruity, cool, and refreshing to eat and is widely loved by consumers worldwide. The single fruit weight is an important factor affecting the yield, and thus the income and economic benefits, of melon crops. In this study, to identify the main QTLs (quantitative trait locus) controlling the single fruit weight of melon and thereby identify candidate genes controlling this trait, specific-locus amplified fragment sequencing (SLAF) analysis was performed on the offspring of female 1244 plants crossed with male MS-5 plants. A total of 115 individual plants in the melon F2 population were analyzed to construct a genetic linkage map with a total map distance of 1383.88 cM by the group in the early stages of the project, which was divided into 12 linkage groups with a total of 10,596 SLAF markers spaced at an average genetic distance of 0.13 cM. A total of six QTLs controlling single fruit weight (sfw loci) were detected. Seven pairs of markers with polymorphisms were obtained by screening candidate intervals from the SLAF data. The primary QTL sfw2.2 was further studied in 300 F2:3 family lines grown in 2020 and 2021, respectively, a positioning sfw2.2 between the markers CY Indel 11 and CY Indel 16, between 18,568,142 and 18,704,724 on chromosome 2. This interval contained 136.58 kb and included three genes with functional annotations, MELO3C029673, MELO3C029669, and MELO3C029674. Gene expression information for different fruit development stages was obtained from 1244 and MS-5 fruits on the 15d, 25d, and 35d after pollination, and qRT-PCR (quantitative reverse transcription-PCR) indicated that the expression of the MELO3C029669 gene significantly differed between the parents during the three periods. The gene sequences between the parents of MELO3C029669 were analyzed and compared, a base mutation was found to occur in the intronic interval between the parents of the gene, from A-G. Phylogenetic evolutionary tree analysis revealed that the candidate gene MELO3C029669 is most closely related to Pisum sativum Fimbrin-5 variant 2 and most distantly related to Cucumis melo var. makuwa. Therefore, it was hypothesized that MELO3C029669 is the primary major locus controlling single fruit weight in melon. These results not only provide a theoretical basis for further studies to find genes with functions in melon single fruit weight but also lay the foundation for accelerating breakthroughs and innovations in melon breeding.

Identification of Key Genes of Fruit Shape Variation in Jujube with Integrating Elliptic Fourier Descriptors and Transcriptome

Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) for gene discovery remain scarce. In this study, six cultivars of jujube fruits with distinct shapes were selected, and samples were collected from the fruit set period to the white mature stage across five time points for shape analysis and transcriptome studies. By combining EFDs with WGCNA and STEM, the study aimed to identify the critical periods and key genes involved in the formation of jujube fruit shape. The findings indicated that the D25 (25 days after flowering) is crucial for the development of jujube fruit shape. Moreover, ZjAGL80, ZjABI3, and eight other genes have been implicated to regulate the shape development of jujubes at different periods of fruit development, through seed development and fruit development pathway. In this research, EFDs were employed to precisely delineate the shape of jujube fruits. This approach, in conjunction with transcriptome, enhanced the precision of gene identification, and offered an innovative methodology for fruit shape analysis. This integration facilitates the advancement of research into the morphological characteristics of plant fruits, underpinning the development of a refined framework for the genetic underpinnings of fruit shape variation.

Cytological, Phytohormone, and Transcriptome Analyses Provide Insights into Persimmon Fruit Shape Formation (Diospyros kaki Thunb.)

Fruit shape is an important external feature when consumers choose their preferred fruit varieties. Studying persimmon (Diospyros kaki Thunb.) fruit shape is beneficial to increasing its commodity value. However, research on persimmon fruit shape is still in the initial stage. In this study, the mechanism of fruit shape formation was studied by cytological observations, phytohormone assays, and transcriptome analysis using the long fruit and flat fruit produced by 'Yaoxianwuhua' hermaphroditic flowers. The results showed that stage 2-3 (June 11-June 25) was the critical period for persimmon fruit shape formation. Persimmon fruit shape is determined by cell number in the transverse direction and cell length in the longitudinal direction. High IAA, GA4, ZT, and BR levels may promote long fruit formation by promoting cell elongation in the longitudinal direction, and high GA3 and ABA levels may be more conducive to flat fruit formation by increasing the cell number in the transverse direction and inhibiting cell elongation in the longitudinal direction, respectively. Thirty-two DEGs related to phytohormone biosynthesis and signaling pathways and nine DEGs related to cell division and cell expansion may be involved in the persimmon fruit shape formation process. These results provide valuable information for regulatory mechanism research on persimmon fruit formation.

Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume)

The Japanese apricot (Prunus mume) is a popular fruit tree in Japan. However, the genetic factors associated with fruit trait variations are poorly understood. In this study, we investigated nine fruit-associated traits, including harvesting time, fruit diameter, fruit shape, fruit weight, stone (endocarp) weight, ratio of stone weight to fruit weight, and rate of fruit gumming, using 110 Japanese apricot accessions over four years. A genome-wide association study (GWAS) was performed for these traits and strong signals were detected on chromosome 6 for harvesting time and fruit diameters. These peaks were shown to undergo strong artificial selection during the differentiation of small-fruit cultivars. The genomic region defined by the GWAS and XP-nSL analyses harbored several candidate genes associated with plant hormone regulation. Furthermore, the alleles of small-fruit cultivars in this region were shown to have genetic proximity to some Chinese cultivars of P. mume. These results indicate that the small-fruit trait originated in China; after being introduced into Japan, it was preferred and selected by the Japanese people, resulting in the differentiation of small-fruit cultivars.

Molecular and genetic regulations of fleshy fruit shape and lessons from Arabidopsis and rice

Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference. Thus, modification of fruit shape has become one of the major objectives for crop improvement. However, the underlying mechanisms of fruit shape regulation are poorly understood. In this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato, cucumber, and peach as examples. Comparative analyses suggest that the OFP-TRM (OVATE Family Protein - TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit species. Interestingly, cucumber homologs of FRUITFULL (FUL1), CRABS CLAW (CRC) and 1-aminocyclopropane-1-carboxylate synthase 2 (ACS2) were found to regulate fruit elongation. We also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice, and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones, including brassinosteroids, gibberellic acids, and auxin, and microtubule organization. In addition, functional redundancy and divergence of the members of each of the OFP, TRM, and IQD families are also shown. This review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.

Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities

Climate change, large monocultures of disease-susceptible cultivars, overuse of pesticides, and the emergence of new pathogens or pathogenic strains causing economic losses are all major threats to our environment, health, food, and nutritional supply. Temperate tree fruit crops belonging to the Rosaceae family are the most economically important and widely grown fruit crops. These long-lived crops are under attack from many different pathogens, incurring major economic losses. Multiple chemical sprays to control various diseases annually is a common practice, resulting in significant input costs, as well as environmental and health concerns. Breeding for disease resistance has been undertaken primarily in pome fruit crops (apples and pears) for a few fungal and bacterial diseases, and to a lesser extent in some stone fruit crops. These breeding efforts have taken multiple decades due to the biological constraints and complex genetics of these tree fruit crops. Over the past couple of decades, major advances have been made in genetic and physical mapping, genomics, biotechnology, genome sequencing, and phenomics, along with accumulation of large germplasm collections in repositories. These valuable resources offer opportunities to make significant advances in greatly reducing the time needed to either develop new cultivars or modify existing economic cultivars for enhanced resistance to multiple diseases. This review will cover current knowledge, challenges, and opportunities in breeding for disease resistance in temperate tree fruit crops.

VvSUN may act in the auxin pathway to regulate fruit shape in grape

Fruit shape is an essential agronomic feature in many crops. We identified and functionally characterized an auxin pathway-related gene, VvSUN. VvSUN, which belongs to the SUN/IQ67-DOMAIN (IQD) family, localizes to the plasma membrane and chloroplast and may be involved in controlling fruit shape through auxin. It is highly expressed in the ovary, and the expression level 1 week before the anthesis stage is positively correlated with the fruit shape index. Functional analyses illustrated that VvSUN gene overexpression in tomato and tobacco plants changed fruit/pod shape. The VvSUN promoter directly bound to VvARF6 in yeast and activated ß-glucuronidase (GUS) activity by indole-3-acetic acid (IAA) treatments in grapevine leaves, indicating that VvSUN functions are in coordination with auxin. Further analysis of 35S::VvSUN transgenic tomato ovaries showed that the fruit shape changes caused by VvSUN were predominantly caused by variations in cell number in longitudinal directions by regulating endogenous auxin levels via polar transport and/or auxin signal transduction process variations. Moreover, enrichment of the 35S::VvSUN transgenic tomato differentially expressed genes was found in a variety of biological processes, including primary metabolic process, transmembrane transport, calcium ion binding, cytoskeletal protein binding, tubulin binding, and microtubule-based movement. Using weighted gene co-expression network analysis (WGCNA), we confirmed that this plant hormone signal transduction may play a crucial role in controlling fruit shape. As a consequence, it is possible that VvSUN acts as a hub gene, altering cellular auxin levels and the plant hormone signal transduction pathway, which plays a role in cell division patterns, leading to anisotropic growth of the ovary and, ultimately, an elongated fruit shape.

Assessment of Various Machine Learning Models for Peach Maturity Prediction Using Non-Destructive Sensor Data

To date, many machine learning models have been used for peach maturity prediction using non-destructive data, but no performance comparison of the models on these datasets has been conducted. In this study, eight machine learning models were trained on a dataset containing data from 180 ‘Suncrest’ peaches. Before the models were trained, the dataset was subjected to dimensionality reduction using the least absolute shrinkage and selection operator (LASSO) regularization, and 8 input variables (out of 29) were chosen. At the same time, a subgroup consisting of the peach ground color measurements was singled out by dividing the set of variables into three subgroups and by using group LASSO regularization. This type of variable subgroup selection provided valuable information on the contribution of specific groups of peach traits to the maturity prediction. The area under the receiver operating characteristic curve (AUC) values of the selected models were compared, and the artificial neural network (ANN) model achieved the best performance, with an average AUC of 0.782. The second-best machine learning model was linear discriminant analysis with an AUC of 0.766, followed by logistic regression, gradient boosting machine, random forest, support vector machines, a classification and regression trees model, and k-nearest neighbors. Although the primary parameter used to determine the performance of the model was AUC, accuracy, F1 score, and kappa served as control parameters and ultimately confirmed the obtained results. By outperforming other models, ANN proved to be the most accurate model for peach maturity prediction on the given dataset.

Construction of a collection of introgression lines of "Texas" almond DNA fragments in the "Earlygold" peach genetic background

Peach [Prunus persica L. Batsch] is one of the major temperate fruit tree species, the commercial materials of which have a low level of genetic variability. Almond [P. dulcis (Mill) DA Webb], a close relative of peach cultivated for its kernels, has a much higher level of diversity. The species are inter-compatible and often produce fertile hybrids, almond being a possible source of new genes for peach that could provide biotic and abiotic stress tolerance traits. In this paper we describe the development of a collection of peach-almond introgression lines (ILs) having a single fragment of almond (cv. Texas) in the peach background (cv. Earlygold). Lines with few introgressions were selected with markers from successive generations from a "Texas" × "Earlygold" F1 hybrid, initially using a set of SSRs and later with the 18 k peach SNP chip, allowing for the final extraction of 67 lines, 39 with almond heterozygous introgressions covering 99% of the genome, and 28 with homozygous introgressions covering 83% of the genome. As a proof of concept, four major genes and four quantitative characters were examined in the selected ILs giving results generally consistent with previous information on the genetics of these characters. This collection is the first of its kind produced in a woody perennial species and promises to be a valuable tool for genetic analyses, including dissection of quantitative traits, positional cloning, epistasis and as prebreeding material to introgress almond genes of interest into the peach commercial gene pool.