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Pseudomonas syringae pv. tomato (Pst) is the causal agent of bacterial speck disease in tomatoes. The Pto/Prf gene cluster from Solanum pimpinellifolium was introgressed into several modern tomato cultivars and provided protection against Pst race 0 strains for many decades. However, virulent Pst race 1 strains that evade Pto -mediated immunity now predominate in tomato-growing regions worldwide. Here we report the identification of resistance to a Pst race 1 strain (Pst 19) in the wild tomato accession S. pimpinellifolium LA1589 (hereafter LA1589), using our rapid high-throughput seedling screen. LA1589 supports less bacterial growth than cultivars, and does not exhibit a hypersensitive response to Pst 19. We tested an existing set of 87 Inbred Backcross Lines (IBLs) derived from a cross between susceptible Solanum lycopersicum E-6203 and Solanum pimpinellifolium LA1589 for resistance to Pst 19. Using single-marker analysis, we identified three genomic regions associated with resistance. Bacterial growth assays on IBLs confirmed that these regions contribute to resistance in planta. We also mapped candidate genes associated with resistance in a cross between the Solanum lycopersicum var. lycopersicum cultivar Heinz BG-1706 and S. pimpinellifolium LA1589. By comparing candidates from the two mapping approaches, we were able to identify 3 QTL and 5 candidate genes in LA1589 for a role in resistance to Pst 19. This work will assist in molecular marker-assisted breeding to protect tomato from bacterial speck disease. [ABSTRACT FROM AUTHOR]

Background: Melon (Cucumis melo L.), an important cucurbit crop, faces production limitations due to powdery mildew (PM). Developing resistant varieties offers a sustainable, genetics-based alternative to chemical treatments. Therefore, identifying PM resistance quantitative trait loci (QTL) and creating trait-associated markers are essential for efficient melon PM resistance improvement through marker-assisted backcrossing (MABC). Results: Three F2 populations, A6, B2, and C4, were generated for QTL mapping of PM resistance. Major QTL were identified on chromosome 2 in A6, chromosome 5 in B2, and chromosomes 5 and 12 in C4. A series of TaqMan® assays targeting regions on chromosomes 2, 5, and 12 were developed and validated for foreground and recombinant selection, complemented by the double digest restriction-site associated DNA genotyping system to evaluate the recurrent parent genome recovery. Three MABC programs using resistant donor parents from A6 and C4 crossed with elite susceptible recurrent parents with green and orange fruit flesh were implemented. After two to three cycles of MABC, individual QTL was successfully introgressed into elite genetic backgrounds, giving six PM resistance lines in each green- and orange-fleshed background. PM inoculation on the twelve near-isogenic lines confirmed their resistance to PM. Conclusions: We have identified major PM resistance QTL for melon on chromosomes 2, 5, and 12 and have introgressed individual QTL to elite genetic backgrounds using MABC in three and a half years. This study demonstrates the power of combining high-throughput genotyping with breeding efforts and showcases the efficiency of molecular breeding. [ABSTRACT FROM AUTHOR]

Optimizing plant nitrogen (N) usage and inhibiting N leaching loss in the soil–crop system is crucial to maintaining crop yield and reducing environmental pollution. This study aimed at identifying quantitative trait loci (QTLs) and differentially expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterized a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in a greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population. Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven QTLs were detected for three target traits (leaf N content, leaf nitrogen balance index, and petiole NO3− content), 10 and six in the low and high N condition, respectively, while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4752 and 2405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3628 (50.6%) in leaves and 1717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1677 DEGs were shared between organs or tissues. Finally, we integrated DEG and QTL analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding tomato varieties requiring less N input. [ABSTRACT FROM AUTHOR]

Over the centuries, strawberry fruit quality has greatly improved through various selection studies. The discovery of genes and genomic positions related to traits such as fruit quality and resistance to diseases and pests has been accelerated by new biotechnological methods. The objectives of this study are (i) to construct single nucleotide polymorphism (SNP) Fana array-based high-throughput genetic linkage groups for the 'Fortuna × Rubygem' F1 population, and (ii) to detect quantitative trait loci (QTL) regions associated with Botrytis cinerea resistance in leaf and fruit traits of strawberry. A total of 945 and 984 SNPs were mapped in the 'Fortuna' maternal and the 'Rubygem' paternal maps, respectively. The lengths of the linkage groups (LGs) and the average length of 'Fortuna' were calculated to be 1814 cM and 55.0 cM, respectively. The total length of 'Rubygem' was determined to be 2170 cM, with an average length of 65.7 cM. The average marker densities for the'Fortuna' and 'Rubygem' linkages per cM were recorded as 0.58 and 0.53 markers, respectively. The 'Fortuna' female produced a mean of 28.64 markers per LG, while the 'Rubygem' male linkage groups had approximately 30 markers per LG. Five significant QTLs associated with resistance to B. cinerea in the leaves were identified in both parents. QTLs associated with resistance in strawberry fruits were found within a total of three LGs in different positions. The compressive genetic linkage maps developed in 'Fortuna × Rubygem' population can be used in genetic and QTL studies for important agronomical traits. The identified QTLs associated with Botrytis cinerea resistance may be preferred for use in future strawberry breeding programs to carry out markerassisted selection. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments. [ABSTRACT FROM AUTHOR]

Abstract Background Melon (Cucumis melo L.), an important cucurbit crop, faces production limitations due to powdery mildew (PM). Developing resistant varieties offers a sustainable, genetics-based alternative to chemical treatments. Therefore, identifying PM resistance quantitative trait loci (QTL) and creating trait-associated markers are essential for efficient melon PM resistance improvement through marker-assisted backcrossing (MABC). Results Three F2 populations, A6, B2, and C4, were generated for QTL mapping of PM resistance. Major QTL were identified on chromosome 2 in A6, chromosome 5 in B2, and chromosomes 5 and 12 in C4. A series of TaqMan® assays targeting regions on chromosomes 2, 5, and 12 were developed and validated for foreground and recombinant selection, complemented by the double digest restriction-site associated DNA genotyping system to evaluate the recurrent parent genome recovery. Three MABC programs using resistant donor parents from A6 and C4 crossed with elite susceptible recurrent parents with green and orange fruit flesh were implemented. After two to three cycles of MABC, individual QTL was successfully introgressed into elite genetic backgrounds, giving six PM resistance lines in each green- and orange-fleshed background. PM inoculation on the twelve near-isogenic lines confirmed their resistance to PM. Conclusions We have identified major PM resistance QTL for melon on chromosomes 2, 5, and 12 and have introgressed individual QTL to elite genetic backgrounds using MABC in three and a half years. This study demonstrates the power of combining high-throughput genotyping with breeding efforts and showcases the efficiency of molecular breeding.

Abstract Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2 LOC_Os05g09520 . These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor.

Light is a crucial environmental factor that influences the phenotypic development of plants. Despite extensive studies on the physiological, biochemical, and molecular mechanisms of the impact of light on phenotypes, genetic investigations regarding light-induced transgenerational plasticity in Arabidopsis thaliana remain incomplete. In this study, we used thaliana as the material, then gathered phenotypic data regarding leaf number and plant height under high- and low-light conditions from two generations. In addition to the developed genotype data, a functional mapping model was used to locate a series of significant single-nucleotide polymorphisms (SNPs). Under low-light conditions, a noticeable adaptive change in the phenotype of leaf number in the second generation suggests the presence of transgenerational genetic effects in thaliana under environmental stress. Under different lighting treatments, 33 and 13 significant genes associated with transgenerational inheritance were identified, respectively. These genes are largely involved in signal transduction, technical hormone pathways, light responses, and the regulation of organ development. Notably, genes identified under high-light conditions more significantly influence plant development, whereas those identified under low-light conditions focus more on responding to external environmental stimuli.

Abstract Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.

ABSTRACT Investigating the inheritance and genetic variation of luteolin content in peanut shells is pivotal for developing improved cultivars with high luteolin content. In this study, we developed a genetic map spanning 976.8 cM using 115 highly advanced recombinant inbred lines (RILs) and the Axiom_Arachis array containing 58K single‐nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) analysis was then performed using phenotype data from 2‐year field trials. From these analyses, we identified three significant QTLs with 4.1%–11.7% phenotypic variation explained (PVE) for luteolin content in peanut shells. We further identified five candidate genes with putative functions suggesting possible involvement in plant flavonoid and terpenoid biosynthetic pathways in peanut luteolin biosynthesis. Additionally, two new peanut inbreeding lines with high luteolin and oleic acid levels were selected and are expected to be used as multifunctional genomic backgrounds for future breeding and research programs. The information on the QTL regions and candidate genes from the present study could be very useful for developing new peanut cultivars with high luteolin content and for identifying the genetic/genomic determinants of luteolin content in peanut shells. [ABSTRACT FROM AUTHOR]

Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2LOC_Os05g09520. These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor. [ABSTRACT FROM AUTHOR]

Many traits play essential roles in determining crop yield. Wide variation for morphological traits exists in Hordeum vulgare L., but the genetic basis of this morphological variation is largely unknown. To understand genetic basis controlling morphological traits affecting yield, a barley doubled haploid population (146 individuals) derived from Clipper X Sahara 3771 was used to map chromosome regions underlying days to awn appearance, plant height, fertile spike number, flag leaf length, spike length, harvest index, seed number per plant, thousands kernel weight, and grain yield. Twentyseven QTLs for nine traits were mapped to the barley genome that described 3-69% of phenotypic variations; and some genomic regions harbor a given QTL for more than one trait. Out of 27 QTLs identified, 19 QTLs were novel. Chromosomal regions on 1H, 2H, 4H, and 6H associated with seed grain yield, and chromosome regions on 2H and 6H had major effects on grain yield (GY). One major QTL for seed number per plant was flanked by marker VRS1-KSUF15 on chromosome 2H. This QTL was also associated with GY. Some loci controlling thousands kernel weight (TKW), fertile spike number (FSN), and GY were the same. The major grain yield QTL detected on linkage PSR167 co-localized with TAM10. Two major QTLs controlling TKW and FSN were also mapped at this locus. Eight QTLs on chromosomes 1H, 2H, 3H, 4H, 5H, 6H, and 7H consistently affected spike characteristics. One major QTL (ANIONT1A-TACMD) on 4H affected both spike length (SL) and spike number explained 9 and 5% of the variation of SL and FSN, respectively. In conclusion, this study could cast some light on the genetic basis of the studied pivotal traits. Moreover, fine mapping of the identified major effect markers may facilitate the application of molecular markers in barley breeding programs. [ABSTRACT FROM AUTHOR]

Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice. [ABSTRACT FROM AUTHOR]

IntroductionPowdery mildew (PM) poses an extreme threat to wheat yields and quality.[Methods] In this study, 262 recombinant inbred lines (RILs) of Doumai and Shi 4185 cross were used to map PM resistance genes across four environments. A high-density genetic linkage map of the Doumai/Shi 4185 RIL population was constructed using the wheat Illumina iSelect 90K single-nucleotide polymorphism (SNP) array.ResultsIn total, four stable quantitative trait loci (QTLs) for PM resistance, QPm.caas-2AS, QPm.caas-4AS, QPm.caas-4BL, and QPm.caas-6BS, were detected and explained 5.6%–15.6% of the phenotypic variances. Doumai contributed all the resistance alleles of QPm.caas-2AS, QPm.caas-4AS, QPm.ca as-4BL, and QPm.caas-6BS. Among these, QPm.caas-4AS and QPm.caas-6BS overlapped with the previously reported loci, whereas QPm.caas-2AS and QPm.caas-4BL are potentially novel. Additionally, six high-confidence genes encoding the NBS-LRR-like resistance protein, disease resistance protein family, and calcium/calmodulin-dependent serine/threonine-kinase were selected as the candidate genes for PM resistance. Three kompetitive allele-specific PCR (KASP) markers, Kasp_PMR_2AS for QPm.caas-2AS, Kasp_PMR_4BL for QPm.caas-4BL, and Kasp_PMR_6BS for QPm.caas-6BS, were developed, and their genetic effects were validated in a natural population including 100 cultivars.DiscussionThese findings will offer valuable QTLs and available KASP markers to enhance wheat marker-assisted breeding for PM resistance.

Pseudomonas syringae pv. tomato (Pst) is the causal agent of bacterial speck disease in tomatoes. The Pto/Prf gene cluster from Solanum pimpinellifolium was introgressed into several modern tomato cultivars and provided protection against Pst race 0 strains for many decades. However, virulent Pst race 1 strains that evade Pto-mediated immunity now predominate in tomato-growing regions worldwide. Here we report the identification of resistance to a Pst race 1 strain (Pst19) in the wild tomato accession S. pimpinellifolium LA1589 (hereafter LA1589), using our rapid high-throughput seedling screen. LA1589 supports less bacterial growth than cultivars, and does not exhibit a hypersensitive response to Pst19. We tested an existing set of 87 Inbred Backcross Lines (IBLs) derived from a cross between susceptible Solanum lycopersicum E-6203 and Solanum pimpinellifolium LA1589 for resistance to Pst19. Using single-marker analysis, we identified three genomic regions associated with resistance. Bacterial growth assays on IBLs confirmed that these regions contribute to resistance in planta. We also mapped candidate genes associated with resistance in a cross between the Solanum lycopersicum var. lycopersicum cultivar Heinz BG-1706 and S. pimpinellifolium LA1589. By comparing candidates from the two mapping approaches, we were able to identify 3 QTL and 5 candidate genes in LA1589 for a role in resistance to Pst19. This work will assist in molecular marker-assisted breeding to protect tomato from bacterial speck disease.

Millets are small-seeded cereals belonging to the family Poaceae. They are considered to be climate-resilient and future nutritional food cereals for humans. Millets are resistant to biotic and abiotic stressors compared to other major cereals and thrive in low-quality soils with little maintenance and less rainfall. The importance of millets is still not well known to many people due to the lack of popularity and cultivation in semi-arid tropics of Asia and Africa. The United Nations has declared 2023 as the International Year of Millets (IYM 2023) to promote millet cultivation and popularize their health benefits globally. A few years ago, the application of molecular biology was in its infancy in millets due to the unavailability of genome sequences. Genome sequences are available for most of the millets on NCBI and Phytozome databases. In this review, we discuss the details of genome sequences for millets, candidate genes identified from the native genome of millets. The current status of quantitative trait loci and genome-wide association studies in millets are also discussed. The utilization of millet genome sequences in functional genomics research and translating the information for crop improvement will help millet and non-millet cereals survive harsh environments in the future. Such efforts will help strengthen food security and reduce malnutrition worldwide in 2050. [ABSTRACT FROM AUTHOR]

The utilization of high-throughput data sequencing has been instrumental in the generation of extensive datasets derived from diverse studies, with a primary focus on elements such as epigenetics, genomic variations, genome-wide associations, and differential gene expression in the context of bull fertility. However, the task of achieving effective prediction remains a formidable challenge. The current investigation aims to examine variations identified through RNA-Seq, with a particular emphasis on coding region alterations, and subsequently, map these variations to the region of genes associated with fertility functions and proximity. In this study, transcriptome analysis was carried over sperm samples obtained from 12 bulls, half of which exhibited high fertility (n=6) and the other half low fertility (n=6) based on their conception rates. Bioinformatics tools align the data; genetic variants were identified and mapped subsequently to known fertility quantitative trait loci (QTL). After filtering for fertility-specific single nucleotide polymorphisms (SNPs) with missense mutations, we identified a total of six significant biomarkers. This research demonstrates the efficacy of our innovative approach for screening genetic variants, ultimately leading to the identification of fertility markers within bovine spermatozoa. [ABSTRACT FROM AUTHOR]

Italian ryegrass (Lolium multiflorum Lam.; IRG), an important Lolium species, is mainly cultivated in South Korea, Japan, China, and used as forage (pastes, hay, silage). Another important species of Lolium are perennial ryegrass (Lolium perenne L.; PRG), which is cultivated in Europe, United States of America, Australia, and New Zealand. The main character of the genus Lolium, which includes IRG and PRG, is its palatability; however, Lolium species exhibit summer depression during hot summers. The breeding goal of Festulolium, an interspecific and generic hybridization product of Lolium and Festuca, is to overcome the shortcomings of Lolium species. As such, pasture breeding is same varieties because polycrossing methods are used as five or more genetic resources, but there are some differences within the individual varieties. Amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers are used to investigate the geographical origins, ploidy levels, biological status, donor information, and flowering seasons of these varieties. Genetic markers are also used to construct linkage maps. Based on linkage map analyses, studies of Lolium quantitative trait loci (QTL) contributed to the breeding of varieties with improved tolerance or resistance to biological and non-biological stress factors. In this study, we summarize recent studies on the cultivation status of IRG in South Korea, linkage mapping of Lolium, and associated QTL analyses. We also discuss interspecific and generic hybridization of Lolium and Festuca. [ABSTRACT FROM AUTHOR]

Growth traits are economically important characteristics for the genetic improvement of local cattle breeds. Genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to perform a GWAS to identify genomic regions and genes associated to birth weight, weaning weight adjusted for 240 days, 16 months, and 24 months weight in Romosinuano (ROMO) and Blanco Orejinegro (BON) cattle. A single-step genomic-BLUP was implemented using 596 BON and 569 ROMO individuals that were genotyped with an Illumina BovineSNP50 BeadChip. There were 25 regions of interest identified on different chromosomes, with few of them simultaneously associated with two or more growth traits and some were common to both breeds. The gene mapping allowed to find 173 annotations on these regions, from which 49 represent potential candidate genes with known growth-related functions in cattle and other species. Among the regions that were associated with several growth traits, that at 24 – 27 MB of BTA14, has important candidate genes such as LYPLA1, XKR4, TMEM68 and PLAG1. Another region of interest at 0.40–0.77 Mb of BTA23 was identified in both breeds, containing KHDRBS2 as a potential candidate gene influencing body weight. Future studies targeting these regions could provide more knowledge to uncover the genetic architecture underlying growth traits in BON and ROMO cattle. The genomic regions and genes identified in this study could be used to improve the prediction of genetic merit for growth traits in these creole cattle breeds. [ABSTRACT FROM AUTHOR]

Flax powdery mildew (PM), caused by Oidium lini, is a globally distributed fungal disease of flax, and seriously impairs its yield and quality. To data, only three resistance genes and a few putative quantitative trait loci (QTL) have been reported for flax PM resistance. To dissect the resistance mechanism against PM and identify resistant genetic regions, based on four years of phenotypic datasets (2017, 2019 to 2021), a genome-wide association study (GWAS) was performed on 200 flax core accessions using 674,074 SNPs and 7 models. A total of 434 unique quantitative trait nucleotides (QTNs) associated with 331 QTL were detected. Sixty-four loci shared in at least two datasets were found to be significant in haplotype analyses, and 20 of these sites were shared by multiple models. Simultaneously, a large-effect locus (qDI 11.2) was detected repeatedly, which was present in the mapping study of flax pasmo resistance loci. Oil flax had more QTL with positive-effect or favorable alleles (PQTL) and showed higher PM resistance than fiber flax, indicating that effects of these QTL were mainly additive. Furthermore, an excellent resistant variety C120 was identified and can be used to promote planting. Based on 331 QTLs identified through GWAS and the statistical model GBLUP, a genomic selection (GS) model related to flax PM resistance was constructed, and the prediction accuracy rate was 0.96. Our results provide valuable insights into the genetic basis of resistance and contribute to the advancement of breeding programs.

Drought is a misfortune for crops. Wheat is a staple crop and its sustainability and adequate supply are vital to food security around the world. The development of drought-tolerant cultivars in wheat is a major challenge to breeders, therefore there is dire need of time to determine the genetic components of drought tolerance in wheat crop. To overcome intense drought stress, wheat plants undergo certain morphological and physiological changes and develop certain genetically adaptive mechanisms. Since wheat is an allotriploid with three sub-genomes, its adaptability molecular mechanisms to drought, particularly needs scientific attention. Here, we systematically and comprehensively reviewed the causes of wheat drought tolerance and the consequences for wheat physiology and genetics. The quantitative trait loci (QTL), which be function on the control of wheat drought tolerance, were comprehensively summarized by a meta-analysis and total 75 meta-QTLs (MQTLs) were identified. In addition, we summarized the genes tightly involved in wheat drought tolerance, and several important genes were selected to elucidate signaling networks related to the wheat drought tolerance. This review is integral to growing suitable strains in the worldwide arid regions to improve wheat yields under recent global climate change scenarios.

Ankamali pig is a domesticated native variety of Kerala which is well known for its disease resistance, lean meat and adaptability to hot tropical environments. Recent breakthrough in genome sequencing technologies have created unparalleled prospects to characterize individual genomic landscapes and identifying mutations between and within populations. The current study aims to determine the genetic variations in Ankamali pigs using whole genome sequencing. The GATK HaplotypeCaller was used to identify the variants. There were over 26 million (26,604,589) single nucleotide variants (SNVs), including more than 21 million SNPs and over 5 million indels. In Ankamali pigs, the total genome length obtained was more than 2.5 billion with an average variant rate of one variant in every 94 bases. The significance of different variant rate on 18 chromosomes were analysed using the chi-square statistics. The variant rates in Sus scrofa chromosomes10 and 13 were significantly different (p

Low soil nitrogen levels, compounded by the high costs associated with nitrogen supplementation through fertilizers, significantly contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). The discovery of genomic regions associated with low nitrogen tolerance in maize can enhance selection efficiency and facilitate the development of improved varieties. To elucidate the genetic architecture of grain yield (GY) and its associated traits (anthesis-silking interval (ASI), anthesis date (AD), plant height (PH), ear position (EPO), and ear height (EH)) under different soil nitrogen regimes, four F3 maize populations were evaluated in Kenya and Zimbabwe. GY and all the traits evaluated showed significant genotypic variance and moderate heritability under both optimum and low nitrogen stress conditions. A total of 91 quantitative trait loci (QTL) related to GY (11) and other secondary traits (AD (26), PH (19), EH (24), EPO (7) and ASI (4)) were detected. Under low soil nitrogen conditions, PH and ASI had the highest number of QTLs. Furthermore, some common QTLs were identified between secondary traits under both nitrogen regimes. These QTLs are of significant value for further validation and possible rapid introgression into maize populations using markerassisted selection. Identification of many QTL with minor effects indicates genomic selection (GS) is more appropriate for their improvement. Genomic prediction within each population revealed low to moderately high accuracy under optimum and low soil N stress management. However, the accuracies were higher for GY, PH and EH under optimum compared to low soil N stress. Our findings indicate that genetic gain can be improved in maize breeding for low N stress tolerance by using GS. [ABSTRACT FROM AUTHOR]

Introduction: Sclerotinia sclerotiorum is a serious pathogen causing severe basal stalk rot (BSR) disease on cultivated sunflower (Helianthus annuus L.) that leads to significant yield losses due to insufficient resistance. The wild annual sunflower species H. petiolaris, commonly known as prairie sunflower is known for its resistance against this pathogen. Sunflower resistance to BSR is quantitative and determined by many genes with small effects on the resistance phenotype. The objective of this study was to identify loci governing BSR resistance derived from H. petiolaris using a quantitative trait loci (QTL) mapping approach. Methods: BSR resistance among lines of an advanced backcross population (ABQTL) with 174 lines developed from a cross of inbred line HA 89 with H. petiolaris PI 435843 was determined in the field during 2017-2019, and in the greenhouse in 2019. AB-QTL lines and the HA 89 parent were genotyped using genotypingby- sequencing and a genetic linkage map was developed spanning 997.51 cM and using 1,150 SNP markers mapped on 17 sunflower chromosomes. Results and discussion: Highly significant differences (p<0.001) for BSR response among AB-QTL lines were observed disease incidence (DI) in all field seasons, as well as disease rating (DR) and area under the disease progress curve (AUDPC) in the greenhouse with a moderately high broad-sense heritability (H²) of 0.61 for the tested resistance parameters. A total of 14 QTL associated with BSR resistance were identified on nine chromosomes, each explaining a proportion of the phenotypic variation ranging from 3.5% to 28.1%. Of the 14 QTL, eight were detected for BSR resistance in the field and six were detected under greenhouse conditions. Alleles conferring increased BSR resistance were contributed by the H. petiolaris parent at 11 of the 14 QTL. [ABSTRACT FROM AUTHOR]

The high morbidity and mortality rates associated with sepsis highlight the challenges of finding specific remedies for this condition in the intensive care unit (ICU). This study aimed to explore the differentially expressed genes (DEGs) specific to cell types in sepsis and investigate the role of resistin in the survival of sepsis patients through Mendelian randomization (MR) analyses. We used single-cell and bulk transcriptome data to identify cell type-specific DEGs between sepsis and healthy controls. MR analyses were then conducted to investigate the causal relationships between resistin (one of the identified DEGs) levels and the survival of sepsis patients. Additionally, we utilized meQTL (methylation quantitative trait loci) to identify cytosine-phosphate-guanine (CpG) sites that may directly affect sepsis. We identified 560 cell type-specific DEGs between sepsis and healthy controls. Notably, we observed the upregulation of resistin levels in macrophages during sepsis. In bulk transcriptome, RETN is also upregulated in sepsis samples compared with healthy controls. MR analyses revealed a negative association existed between the expression of resistin, at both gene and protein levels, and the mortality or severity of sepsis patients in ICU. Moreover, there were no associations observed between resistin levels and death or organ failure due to other causes. We also identified three methylation CpG sites, located in RETN or its promoter region—cg06633066, cg22322184, and cg02346997—that directly affected both resistin protein levels and sepsis death in the ICU. Our findings suggest that resistin may provide feasible protection for sepsis patients, particularly those with severe cases, without serious side effects. Therefore, resistin could be a potential drug candidate for sepsis treatment. Additionally, we identified two CpG sites, cg06633066 and cg22322184, that were associated with RETN protein levels and sepsis death, providing novel insights into the underlying mechanisms of sepsis. [ABSTRACT FROM AUTHOR]

Abstract Background Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. Results We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. Conclusions Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration.

Millets are small-seeded cereals belonging to the family Poaceae. They are considered to be climate-resilient and future nutritional food cereals for humans. Millets are resistant to biotic and abiotic stressors compared to other major cereals and thrive in low-quality soils with little maintenance and less rainfall. The importance of millets is still not well known to many people due to the lack of popularity and cultivation in semi-arid tropics of Asia and Africa. The United Nations has declared 2023 as the International Year of Millets (IYM 2023) to promote millet cultivation and popularize their health benefits globally. A few years ago, the application of molecular biology was in its infancy in millets due to the unavailability of genome sequences. Genome sequences are available for most of the millets on NCBI and Phytozome databases. In this review, we discuss the details of genome sequences for millets, candidate genes identified from the native genome of millets. The current status of quantitative trait loci and genome-wide association studies in millets are also discussed. The utilization of millet genome sequences in functional genomics research and translating the information for crop improvement will help millet and non-millet cereals survive harsh environments in the future. Such efforts will help strengthen food security and reduce malnutrition worldwide in 2050.

Low soil nitrogen levels, compounded by the high costs associated with nitrogen supplementation through fertilizers, significantly contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). The discovery of genomic regions associated with low nitrogen tolerance in maize can enhance selection efficiency and facilitate the development of improved varieties. To elucidate the genetic architecture of grain yield (GY) and its associated traits (anthesis-silking interval (ASI), anthesis date (AD), plant height (PH), ear position (EPO), and ear height (EH)) under different soil nitrogen regimes, four F3 maize populations were evaluated in Kenya and Zimbabwe. GY and all the traits evaluated showed significant genotypic variance and moderate heritability under both optimum and low nitrogen stress conditions. A total of 91 quantitative trait loci (QTL) related to GY (11) and other secondary traits (AD (26), PH (19), EH (24), EPO (7) and ASI (4)) were detected. Under low soil nitrogen conditions, PH and ASI had the highest number of QTLs. Furthermore, some common QTLs were identified between secondary traits under both nitrogen regimes. These QTLs are of significant value for further validation and possible rapid introgression into maize populations using marker-assisted selection. Identification of many QTL with minor effects indicates genomic selection (GS) is more appropriate for their improvement. Genomic prediction within each population revealed low to moderately high accuracy under optimum and low soil N stress management. However, the accuracies were higher for GY, PH and EH under optimum compared to low soil N stress. Our findings indicate that genetic gain can be improved in maize breeding for low N stress tolerance by using GS.

IntroductionSclerotinia sclerotiorum is a serious pathogen causing severe basal stalk rot (BSR) disease on cultivated sunflower (Helianthus annuus L.) that leads to significant yield losses due to insufficient resistance. The wild annual sunflower species H. petiolaris, commonly known as prairie sunflower is known for its resistance against this pathogen. Sunflower resistance to BSR is quantitative and determined by many genes with small effects on the resistance phenotype. The objective of this study was to identify loci governing BSR resistance derived from H. petiolaris using a quantitative trait loci (QTL) mapping approach.MethodsBSR resistance among lines of an advanced backcross population (AB-QTL) with 174 lines developed from a cross of inbred line HA 89 with H. petiolaris PI 435843 was determined in the field during 2017-2019, and in the greenhouse in 2019. AB-QTL lines and the HA 89 parent were genotyped using genotyping-by-sequencing and a genetic linkage map was developed spanning 997.51 cM and using 1,150 SNP markers mapped on 17 sunflower chromosomes.Results and discussionHighly significant differences (p

Rice drought resistance is a complicated quantitative feature involving a range of biological and agronomic variables, but little is known about the underlying genetics and regulatory mechanisms that regulate drought tolerance. This study used 120 recombinant inbred lines (RILs), derived from a cross between drought tolerant Lvhan 1 and susceptible Aixian 1. The RILs were subjected to drought stress at the first ear stage, and phenotypic data of 16 agronomic and physiological traits under varying conditions were investigated. Genome-wide association study (GWAS) on the drought resistance index of traits was carried out. A total of 9 quantitative trait loci (QTLs) associated with drought-related traits were identified on chromosomes 2, 6, 7, 8, 9, and 10, which includes QTLs for plant height (PH) qPH10.1, effective panicles number (EPN) qEPN6.1, panicle length (PL) qPL9.1, thousand-grain weight (TGW) qTGW2.1, qTGW6.1, qTGW8.1, leaf length (LL) qLL7.1, leaf width (LW) qLW7.1, and leaf area (LA) qLA7.1. The fraction of phenotypic variation explained by individual QTL varied from 10.6% to 13.9%. Except for days to flowering (DTF), the mean values of all traits under normal water management conditions were considerably higher than those under drought conditions. Except for the DTF, the drought resistance index of all rice traits was less than 1, indicating that drought treatment reduced the EPN, FGPP, SSR, PH, and LA, which affected the growth and development of rice. The drought resistance index of DTF was 1.02, indicating that drought prolonged the heading time of rice and diminish the yield parameters. Along with identifying QTLs, the results also predicted ten candidate genes, which are directly or indirectly involved in various metabolic functioning related to drought stress. The identification of these genomic sites or QTLs that effectively respond to water scarcity will aid in the quest of understanding the drought tolerance mechanisms. This study will facilitate the marker-assisted rice breeding and handy in the breeding of drought-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

Blast disease causes serious economic yield losses in pearl millet. Identification and introgression of genomic regions associated with blast resistance can help to develop resistant cultivars to minimize yield losses incurred from blast outbreaks. In this study, 384 advanced pearl millet genotypes were screened against six blast pathotype‐isolates (major pearl millet growing agro‐ecologies of India), namely, Pg 45, Pg 118, Pg 138, Pg 186, Pg 204 and Pg 232. Analysis of variance showed significant (P <.001) variation among genotypes for blast reaction (susceptible to resistance). ICMR 08111 and ICMR 10888 genotypes showed resistance to all six blast pathotypes. A genome‐wide association study performed with 264,241 single nucleotide polymorphic markers could successfully identify 15 SNPs (P = 1.26 × 10−7 to 9.22 × 10−12) underlying the genomic regions governing blast‐resistance across five different chromosomes. The SNPs reported had a significant association in at least two of the three models tested (GLM, MLM and Farm CPU). These SNPs can be used in pearl millet‐resistant breeding programmes after their function has been validated across different genetic backgrounds. [ABSTRACT FROM AUTHOR]

Increasing the epicotyl length (ECL) of adzuki bean cultivars enhances the suitability for mechanical weeding during the vegetative stages and harvesting at pod maturity. To explore the genetic control of ECL, and to identify molecular markers that could facilitate breeding for increased ECL, recombinant inbred lines (RILs) were developed from a cross between Toiku161 (long epicotyls) and Chihayahime (ordinary length epicotyls). In this study, four quantitative trait loci (QTLs) were identified for ECL by QTL-seq analysis, one each on chromosomes 2, 7, 10 and 11. Insertion and deletion (InDel)-based mapping also detected QTLs on chromosomes 7, qECL7.1, and 10, qECL10.1. Substitution mapping using InDel, cleaved amplified polymorphic sequence (CAPS), derived cleaved amplified polymorphic sequence (dCAPS), and single nucleotide polymorphism (SNP) markers narrowed the chromosomal location of qECL7.1 to a 418 kb region flanked by DNA markers TC99_10,211,134 bp and TC102_10,628,880 bp. A total of 35 genes were predicted within the qECL7.1 region. The ECL QTLs and molecular markers identified here will contribute towards marker-assisted selection of desirable long ECL genotypes that allow for increased mechanization and more efficient adzuki bean production. [ABSTRACT FROM AUTHOR]

Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were colocated with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly. [ABSTRACT FROM AUTHOR]

Faba bean (Vicia faba L.) is a valuable legume crop and data on its seed-related traits is required for yield and quality improvements. However, basic research on faba bean is lagging compared to that of other major crops. In this study, an F2 faba bean population, including 121 plants derived from the cross WY7×TCX7, was genotyped using the Faba_bean_130 K targeted next-generation sequencing genotyping platform. The data were used to construct the first ultra-dense faba bean genetic map consisting of 12,023 single nucleotide polymorphisms markers covering 1,182.65 cM with an average distance of 0.098 cM. The map consisted of 6 linkage groups, which is consistent with the 6 faba bean chromosome pairs. A total of 65 quantitative trait loci (QTL) for seedrelated traits were identified (3 for 100-seed weight, 28 for seed shape, 12 for seed coat color, and 22 for nutritional quality). Furthermore, 333 candidate genes that are likely to participate in the regulation of seed-related traits were also identified. Our research findings can provide a basis for future faba bean marker-assisted breeding and be helpful to further modify and improve the reference genome. [ABSTRACT FROM AUTHOR]

The stability of cultivation and production in terms of crop yield has been threatened by climate change due to global warming. Pre-harvest sprouting (PHS) is a threat to crops, especially staple foods, including rice, because of reductions in yield and quality. To address the problem of precocious germination before harvest, we performed quantitative trait loci (QTL) analysis for PHS using F8 RILs populations derived from japonica weedy rice in Korea. QTL analysis revealed that two stable QTLs, qPH7 and qPH2, associated with PHS resistance were identified on chromosomes 7 and 2, respectively, explaining approximately 38% of the phenotypic variation. The QTL effect in the tested lines significantly decreased the degree of PHS, based on the number of QTLs included. Through fine mapping for main QTL qPH7, the region for the PHS was found to be anchored within 23.575–23.785 Mbp on chromosome 7 using 13 cleaved amplified sequence (CAPS) markers. Among 15 open reading frames (ORFs) within the detected region, one ORF, Os07g0584366, exhibited upregulated expression in the resistant donor, which was approximately nine times higher than that of susceptible japonica cultivars under PHS-inducing conditions. Japonica lines with QTLs related to PHS resistance were developed to improve the characteristics of PHS and design practical PCR-based DNA markers for marker-assisted backcrosses of many other PHS-susceptible japonica cultivars. [ABSTRACT FROM AUTHOR]

The pea aphid (PA), Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae), can cause significant damage to dry and green peas, Pisum sativum L. (Fabaceae). Identifying pea lines with resistance to PA is important to advance available control measures. This research identified lines and putative genes with resistance to PA in the USDA Pisum sativum Collection located in Pullman, WA, USA, consisting of 301 lines collected worldwide. Eight commercial pea cultivars were also evaluated. A cluster analysis based on the mean number of adults, nymphs, and total aphids that developed on lines 10 days after the start of infestation by a single adult aphid per plant identified six clusters. Cluster 2, consisting of 48 lines, had the lowest aphid fecundity of all clusters with 2.1 adults, 7.3 nymphs, and 9.4 total aphids produced on average. 'Lifter' was the most resistant line based on low aphid fecundity. Lifter is a white‐flowered green dry pea cultivar that can advance PA resistance in food‐type peas. Genotyping by sequencing based on single‐nucleotide polymorphisms (SNPs) were used in genome‐wide association mapping to locate genes or quantitative trait loci (QTL) linked to PA resistance in which three, nine, and six SNPs were associated with resistance to adult, nymph, and total number of PAs that developed on lines, respectively. Seventeen candidate genes were identified in response to PA resistance. The results can effectively be used in breeding programs to target specific genomic regions with PA resistance and in traditional breeding using resistant lines as parents. [ABSTRACT FROM AUTHOR]

Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively. [ABSTRACT FROM AUTHOR]