QTL analyses of fiber components and crude protein in an annual × perennial ryegrass interspecific hybrid population

Annual (Lolium multiflorum Lam.) and perennial (Lolium perenne L.) ryegrasses are two important forage and turfgrass species. Improving the digestibility of forage by decreasing fiber content is a major goal in forage crop breeding programs. An annual × perennial ryegrass interspecific hybrid population was used to map quantitative trait loci (QTLs) for fiber components, neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL), and crude protein (CP). Samples were harvested three times in August and September 2003 and August 2004, respectively. Simple interval mapping was used to detect QTLs from both the male and female parental maps previously developed for the population. Fiber components were all correlated positively with each other and were negatively correlated with CP. The largest correlations were between NDF and ADF with r = 0.86, 0.72, and 0.82 for each of the three harvests. All four traits showed intermediate broad-sense heritability values ranging from 0.35 to 0.72. A total of 63 QTLs were detected for the four traits measured over the three harvests from both the female and male maps. Coincident QTLs were detected on linkage groups (LGs) 2, 6, and 7 for NDF, LGs 1, 2, and 7 for ADF, LGs 6 and 7 for ADL, and LG 2 for CP, respectively. Coincident QTLs were also detected on LGs 2, 6, and 7 for NDF and ADF, providing evidence of the genetic basis of the observed high level of phenotypic correlation. The QTLs on LGs 2, 6, and possibly 7 for fiber components were co-located on the same LG as several lignin biosynthetic genes from perennial ryegrass.     

Leymus EST linkage maps identify 4NsL-5NsL reciprocal translocation, wheat-Leymus chromosome introgressions, and functionally important gene loci

Allotetraploid (2n = 4x = 28) Leymus triticoides and Leymus cinereus are divergent perennial grasses, which form fertile hybrids. Genetic maps with n = 14 linkage groups (LG) comprised with 1,583 AFLP and 67 heterologous anchor markers were previously used for mapping quantitative trait loci (QTLs) in these hybrids, and chromosomes of other Leymus wildryes have been transferred to wheat. However, identifications of the x = 7 homoeologous groups were tenuous and genetic research has been encumbered by a lack of functional, conserved gene marker sequences. Herein, we mapped 350 simple sequence repeats and 26 putative lignin biosynthesis genes from a new Leymus EST library and constructed one integrated consensus map with 799 markers, including 375 AFLPs and 48 heterologous markers, spanning 2,381 centiMorgans. LG1b and LG6b were reassigned as LG6b* and LG1b*, respectively, and LG4Ns and LG4Xm were inverted so that all 14 linkage groups are aligned to the x = 7 Triticeae chromosomes based on EST alignments to barley and other reference genomes. Amplification of 146 mapped Leymus ESTs representing six of the seven homoeologous groups was shown for 17 wheat-Leymus chromosome introgression lines. Reciprocal translocations between 4L and 5L in both Leymus and Triticum monococcum were aligned to the same regions of Brachypodium chromosome 1. A caffeic acid O-methyltransferase locus aligned to fiber QTL peaks on Leymus LG7a and brown midrib mutations of maize and sorghum. Glaucousness genes on Leymus and wheat chromosome 2 were aligned to the same region of Brachypodium chromosome 5. Markers linked to the S self-incompatibility gene on Leymus LG1a cosegregated with markers on LG2b, possibly cross-linked by gametophytic selection. Homoeologous chromosomes 1 and 2 harbor the S and Z gametophytic self-incompatibility genes of Phalaris, Secale, and Lolium, but the Leymus chromosome-2 self-incompatibility gene aligns to a different region on Brachypodium chromosome 5. Nevertheless, cosegregation of self-incompatibility genes on Leymus presents a powerful system for mapping these loci.     

Gene expression polymorphisms and ESTs associated with gravitropic response of subterranean branch meristems and growth habit in Leymus wildryes

Negatively orthogeotropic (NOGT) tiller and diageotropic (DGT) rhizome meristems develop from the same type of lateral axillary meristems and phytomer structure. Although subterranean NOGT and DGT buds appear similar, they display different responses to gravity and perhaps other cues governing branch angle and overall growth habit (GH). Leymus wildryes show remarkable variation in GH and include some of the largest native grasses in western North America. Previous studies detected GH QTLs on homoeologous regions of LG3a and LG3b controlling differences between caespitose Leymus cinereus and rhizomatous Leymus triticoides allotetraploids. Heterologous barley and wheat microarrays in conjunction with bulk segregate analysis were used to find gene expression polymorphisms associated with GH QTLs. Approximately 34% and 25% of the probe sets showed detectable signals on the barley and wheat arrays, respectively. Overall gene expression patterns of NOGT and DGT meristems were remarkably similar, consistent with the assertion that Leymus NOGT and DGT buds develop from homologous meristems. Only 28 and 27 genes on barley and wheat gene chips, respectively, showed more than twofold differential expressions between NOGT and DGT tissues. One expression polymorphism genetically mapped in the Leymus LG3 rhizome QTL region.     

Genetic relationships between resistance to stalk-tunneling by the European corn borer and cell-wall components in maize population B73×B52

The objective of this study was to assess the relationships among quantitative trait loci (QTL) detected for European corn borer (ECB) tunneling and cell-wall components (CWC) neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL) content in leaf-sheath and stalk tissues in a maize recombinant inbred line population derived from inbred lines B73 and B52. Most of the QTL for ECB resistance (10/13) were at QTL positions for one or more CWC. Of the 12 QTL for NDF and ADF in leaf-sheaths, five for each trait were at or near QTL for ECB tunneling. Four of these five QTL for NDF and ADF mapped to common locations. Four of the eight leaf-sheath ADL QTL were detected in the same genomic regions as ECB QTL. For stalk tissue, four regions contained common/overlapping QTL for ECB tunneling, NDF, and ADF. Six such regions were observed for stalk ADL and ECB tunneling. Seven of the ten QTL associated with both CWC and ECB tunneling contributed to the negative correlations observed between these traits, while relatively few QTL effects were positively correlated. This suggests that while CWC contribute to ECB resistance in this population, other mechanisms and other genes also are involved. Several QTL contributing to the negative correlations between ECB tunneling and CWC in the leaf-sheaths mapped to similar positions as QTL detected in tropical maize populations for resistance to leaf-feeding by Diatraea grandiosella Dyar and Diatraea saccharalis Fabricus. These regions may contain genes involved in the synthesis of cellulose, hemicellulose, and lignin in the leaf-blades and leaf-sheaths of maize.     

BAC library development for allotetraploid Leymus (Triticeae) wildryes enable comparative genetic analysis of lax-barrenstalk1 orthogene sequences and growth habit QTLs

Tall-caespitose basin wildrye (Leymus cinereus) and rhizomatous creeping wildrye (Leymus triticoides) are perennial Triticeae relatives of wheat and barley. Quantitative trait loci (QTLs) controlling rhizome proliferation were previously detected on homoeologous regions of LG3a and LG3b in two full-sib families derived from allotetraploid hybrids. Triticeae homoeologous group 3 aligns to rice chromosome 1, which contains the rice lax panicle and maize barrenstalk1 orthogene responsible for induction of axillary branch meristems, but this gene has not been mapped or sequenced in Triticeae. We developed bacterial artificial chromosome (BAC) libraries representing 6.1 haploid equivalents of the tetraploid Leymus genome (10.7 Mb). Overgo probes designed from the lax-barrenstalk1 orthogene hybridized to 12 Leymus BAC clones. Deduced amino-acid sequences from seven BAC clones were highly conserved with the rice, maize, and sorghum lax-barrenstalk1orthogenes. Gene specific primers designed from two of the most divergent BAC clones map to homoeologous regions of Leymus LG3a and LG3b and align with the lax-barrenstalk1 orthogene on rice 1L. Comparisons of genomic DNA sequences revealed two other conserved regions surrounding the Leymus LG3a, rice, and sorghum lax-barrenstalk1 ortholoci, and one of these regions was also present in maize and Leymus LG3b sequences. Comparisons of Leymus LG3a and LG3b lax-barrenstalk1 coding sequences and flanking genomic regions elucidate molecular differences between subgenomes.     

Genetic mapping and analysis of quantitative trait loci affecting fiber and lignin content in maize

Plant cell walls of forage provide a major source of energy for ruminant animals. Digestion of cell walls is limited by the presence of lignin, therefore the improving the digestibility of forages by reducing lignin content is a major goal in forage crop breeding programs. A recombinant inbred line maize population was used to map quantitative trait loci (QTL) for neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL) of leaf-sheath and stalk tissues. All traits were positively genetically correlated. The larger genetic correlations were between NDF and ADF in sheaths (r = 0.84), NDF and ADF (r = 0.96), ADF and ADL (r = 0.83), and NDF and ADL (r = 0.76) in stalks. Twelve QTL were detected for NDF and 11 QTL for ADF in leaf-sheaths. Eight QTL detected for both traits were defined by the same or linked marker loci. Eight QTL were associated with leaf-sheath ADL. Eleven QTL were detected for NDF and ADF, and 12 QTL for ADL in stalks. Nine of eleven QTL detected for both NDF and ADF in stalks coincided in their genomic position. A high proportion of QTL detected for these traits had the same parental effects and genomic locations, suggesting that it is only necessary to select on one fiber component (NDF or ADF) to improve digestibility. Favorable correlated responses of unselected fiber components are expected due to coincident genomic locations of QTL and the high genetic correlation between fiber components. Several QTL detected in this study coincided in their positions with putative cellulose synthase genes from maize.     

Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in <Emphasis Type="Italic">Eucalyptus nitens</Emphasis> full-sib families

Tree growth and vegetative propagation are complex but important traits under selection in many tree improvement programmes. To understand the genetic control of these traits, we conducted a quantitative trait locus (QTL) study in three full-sib families of Eucalyptus nitens growing at two different sites. One family growing at Ridgley, Tasmania had 300 progeny and two clonally replicated families growing at Mt. Gambier, South Australia had 327 and 210 progeny. Tree growth was measured over several years at both sites and percentages of roots produced by either stem cuttings or tissue culture were assessed in the two Mt. Gambier families. Linkage analysis of growth traits revealed several QTLs for later year traits but few for early year traits, reflecting temporal differences in the heritabilities of these traits. Two growth QTL positions, one on LG8 and another on LG11 were common between the Ridgley and Mt. Gambier families. Four QTLs were observed for each of the two vegetative propagation methods. Two QTLs for vegetative propagation on LG7 and LG11 were validated in the second family at Mt. Gambier. These results suggest that growth and vegetative propagation traits are controlled by several small effect loci. The QTLs identified in this study are useful starting points for identifying candidate genes using the Eucalyptus grandis genome sequence.     

Quantitative trait loci for cell wall components in recombinant inbred lines of maize (Zea mays L.) II: leaf sheath tissue

While maize silage is a significant feed component in animal production operations, little information is available on the genetic bases of fiber and lignin concentrations in maize, which are negatively correlated with digestibility. Fiber is composed largely of cellulose, hemicellulose and lignin, which are the primary components of plant cell walls. Variability for these traits in maize germplasm has been reported, but the sources of the variation and the relationships between these traits in different tissues are not well understood. In this study, 191 recombinant inbred lines of B73 (low-intermediate levels of cell wall components, CWCs) × De811 (high levels of CWCs) were analyzed for quantitative trait loci (QTL) associated with CWCs in the leaf sheath. Samples were harvested from plots at two locations in 1998 and one in 1999 and assayed for neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL). QTL were detected on all ten chromosomes, most in tissue specific clusters in concordance with the high genotypic correlations for CWCs within the same tissue. Adjustment of NDF for its subfraction, ADF, revealed that most of the genetic variation in NDF was probably due to variation in ADF. The low to moderate genotypic correlations for the same CWC across leaf sheath and stalk tissues indicate that some genes for CWCs may only be expressed in certain tissues. Many of the QTL herein were detected in other populations, and some are linked to candidate genes for cell wall carbohydrate biosynthesis.     

QTL analysis and comparative genomics of herbage quality traits in perennial ryegrass (Lolium perenne L.)

Genetic control of herbage quality variation was assessed through the use of the molecular marker-based reference genetic map of perennial ryegrass (Lolium perenne L.). The restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and genomic DNA-derived simple sequence repeat-based (SSR) framework marker set was enhanced, with RFLP loci corresponding to genes for key enzymes involved in lignin biosynthesis and fructan metabolism. Quality traits such as crude protein (CP) content, estimated in vivo dry matter digestibility (IVVDMD), neutral detergent fibre content (NDF), estimated metabolisable energy (EstME) and water soluble carbohydrate (WSC) content were measured by near infrared reflectance spectroscopy (NIRS) analysis of herbage harvests. Quantitative trait locus (QTL) analysis was performed using single-marker regression, simple interval mapping and composite interval mapping approaches, detecting a total of 42 QTLs from six different sampling experiments varying by developmental stage (anthesis or vegetative growth), location or year. Coincident QTLs were detected on linkage groups (LGs) 3, 5 and 7. The region on LG3 was associated with variation for all measured traits across various experimental datasets. The region on LG7 was associated with variation for all traits except CP, and is located in the vicinity of the lignin biosynthesis gene loci xlpomt1 (caffeic acid-O-methyltransferase), xlpccr1 (cinnamoyl CoA-reductase) and xlpssrcad 2.1 (cinnamyl alcohol dehydrogenase). Comparative genomics analysis of these gene classes with wheat (Triticum aestivum L.) provides evidence for conservation of gene order over evolutionary time and the basis for cross-specific genetic information transfer. The identification of co-location between QTLs and functionally associated genetic markers is critical for the implementation of marker-assisted selection programs and for linkage disequilibrium studies, which will enable future improvement strategies for perennial ryegrass.     

大丰野放麇鹿生境中芦苇和互花米草的营养对比分析

2008年9月-2009年7月,对江苏大丰麋鹿国家级自然保护区野放麋鹿生境中食源植物芦苇(Phragmites australis)和互花米草(Spartina alterniflora)的营养成分变化进行了研究;并对5条样线上的样点分别采样,对互花米草和芦苇的粗蛋白、酸性洗涤纤维及中性洗涤纤维分别进行了测定.结果表明:互花米草粗蛋白含量为8.09%,酸性洗涤纤维为36.34%,中性洗涤纤维为69.82%;而芦苇的年度粗蛋白含量为2.84%,酸性洗涤纤维为45.99%,中性洗涤纤维为77.78%;大丰野放麋鹿生境中互花米草的营养成分含量比芦苇高,可见,互花米草是野放麋鹿的喜食植物.     

Quantitative trait loci for cell-wall components in recombinant inbred lines of maize (Zea mays L.) I: stalk tissue

Maize silage is a significant energy source for animal production operations, and the efficiency of the conversion of forage into animal mass is an important consideration when selecting cultivars for use as feed. Fiber and lignin are negatively correlated with digestibility of feed, so the development of forage with reduced levels of these cell-wall components (CWCs) is desirable. While variability for fiber and lignin is present in maize germplasm, traditional selection has focused on the yield of the ear rather than the forage quality of the whole plant, and little information is available concerning the genetics of fiber and lignin. The objectives of this study were to map quantitative trait loci (QTLs) for fiber and lignin in the maize stalk and compare them with QTLs from other populations. Stalk samples were harvested from 191 recombinant inbred lines (RILs) of B73 (an inbred line with low-to-intermediate levels of CWCs) x De811 (an inbred line with high levels of CWCs) at two locations in 1998 and one in 1999 and assayed for neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL). The QTLs were detected on nine chromosomes, mostly clustered in concordance with the high genetic correlations between NDF and ADF. Adjustment of NDF for ADF and ADF for ADL revealed that most of the variability for CWCs in this population is in ADF. Many of the QTLs detected in this study have also been detected in other populations, and several are linked to candidate genes for cellulose or starch biosynthesis. The genetic information obtained in this study should be useful to breeding efforts aimed at improving the quality of maize silage.     

QTL for fibre-related traits in grain × sweet sorghum as a tool for the enhancement of sorghum as a biomass crop

Compared to maize and temperate grasses, sorghum has received less attention in terms of improving cell wall components. The objectives of this study were to identify quantitative trait loci (QTL) with main effects, epistatic and pleiotropic effects along with QTL × environment (QE) interactions controlling fibre-related traits in sorghum. Neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent lignin (ADL), cellulose, hemicellulose, fresh leaf mass, stripped stalk mass, dry stalk mass, fresh biomass and dry biomass were analysed from a population of 188 grain × sweet sorghum recombinant inbred lines. A genetic map consisting of 157 DNA markers was constructed, and QTL were detected using composite interval mapping (CIM). CIM detected more than 5 additive QTL per trait explaining 7.1–24.7% of the phenotypic variation. Abundant co-localization of these QTL was observed across all chromosomes, and the highest cluster was identified on chromosome 6. Searching for candidate genes using the confidence interval of our QTL clusters reveals that these clusters might comprise a set of genes that are tightly linked. Some QTL showed multiple effects; however, the allele for each trait was favouring the parent with the increasing effect. QE interactions were observed for QTL showing multiple effects. Additive × additive interaction was observed for 7 out of 10 traits, indicating the importance of epistatic analysis. However, the phenotypic variation explained by digenic interactions was lower compared to the individual QTL. Our results indicate that various genetic components contribute to fibre-related traits and should be considered during the enhancement of sorghum for lignocellulosic biomass.     

Mapping Genetic Loci for Quantitative Traits of Golden Shell Color,Mineral Element Contents,and Growth-Related Traits in Pacific Oyster (<Emphasis Type="Italic">Crassostrea gigas</Emphasis>)

Golden shell color and mineral content are important economic traits of Pacific oyster (Crassostrea gigas). In this study, we mapped a series of quantitative trait loci (QTLs) that control zinc (Zn) and magnesium (Mg) content, shell color and growth performance to two sex-averaged linkage maps from the FAM-A and FAM-B families. In total, ten QTLs were identified in seven linkage groups (LGs) in the FAM-B family, and seven QTLs were identified in four linkage groups in the FAM-A family. Two QTLs affecting the trait of golden shell color were identified in LG8 of the FAM-A and LG10 of the FAM-B families, which could explain 20.2 and 10.5% of the phenotypic variations, respectively. Two QTLs for Zn content were identified that could contribute to 17.9 and 34.44% of the phenotypic variations in FAM-A. Six QTLs for Zn and Mg contents were identified in four LGs (LG1, LG2, LG5, and LG9) in FAM-B, which explained 13.5–26.7% of the phenotypic variations. In addition, seven QTLs related to oyster growth were recognized in both FAM-A and FAM-B families accounting for 14.6–36.7% of the phenotypic variations. All of the DNA markers in QTL regions were blasted and 14 genes associated with above traits were identified. The mRNA expression of these genes was determined by quantitative RT-PCR. These QTLs and candidate genes could be used as potential targets for marker-assisted selection in C. gigas breeding.     

Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye

Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).     

Phylogenetic relationships among Leymus and related diploid genera (Triticeae: Poaceae) based on chloroplast trnQ–rps16 sequences

To investigate the phylogenetic relationships among Leymus and related diploid genera, the genome donor of Leymus, and the evolutionary history of polyploid Leymus species, chloroplast trnQ–rps16 sequences were analyzed for 36 accessions of Leymus representing 25 species, together with 11 diploid taxa from six monogenomic genera. The phylogenetic analyses (Neighbor‐Joining and MJ network) supported three major clades (Ns, St and Xm). Sequence diversity and genealogical analysis suggested that 1) Leymus species from the same areas or neighboring geographic regions are closely related; 2) most of the Eurasian Leymus species are closely related to Psathyrostachys: P. juncea might serve as the Ns genome donor of polyploid Eurasian Leymus species; 3) the Xm genome may originate from ancestral lineages of Pseudoroegneria (St), Lophopyrum (E^e), Australopyrum (W) and Agropyron (P); 4) the trnQ–rps16 sequences of Leymus are evolutionarily distinct, and may clarify parental lineages and phylogenetic relationships in Leymus.     

玉米自交系秸秆品质性状鉴定与评价

利用近红外漫反射光谱法,对50份常用普通玉米自交系和50份高油自交系秸秆的中性洗涤纤维(NDF)、酸性洗涤纤维(ADF)、可溶性糖(WSC)和粗蛋白(CP)4个品质性状进行了鉴定评价和相关性分析。结果表明,各品质性状变异较大,各性状自交系间差异均达极显著水平。不同品质性状变异程度不同,其中WSC含量变异最大,变异系数达34.23%。WSC与NDF、ADF极显著负相关,NDF与ADF含量极显著正相关。高油系表现为高WSC、CP和低NDF、ADF含量,总体上高油系秸秆品质优于普通玉米。     

Identifying genetic components controlling fertility in the outcrossing grass species perennial ryegrass (Lolium perenne) by quantitative trait loci analysis and comparative genetics

Mutational load and resource allocation factors and their effects on limiting seed set were investigated in ryegrass by comparative mapping genomics and quantitative trait loci (QTL) analysis in two perennial ryegrass (Lolium perenne) mapping families sharing common genetic markers. Quantitative trait loci for seed-set were identified on chromosome (LG) 7 in both families and on LG4 of the F2/WSC family. On LG7, seed-set and heading date QTLs colocalized in both families and cannot be unequivocally resolved. Comparative genomics suggests that the LG7 region is syntenous to a region of rice LG6 which contains both fertility (S5(n)) and heading date (Hd1, Hd3a) candidate genes. The LG4 region is syntenous to a region of rice LG3 which contains a fertility (S33) candidate gene. QTL maxima for seed-set and heading date on LG4 in the F2/WSC family are separated by c. 8 cm, indicating distinct genetic control. Low seed set is under the control of recessive genes at both LG4 and LG7 locations. The identification of QTLs associated with seed set, a major component of seed yield in perennial ryegrass, indicates that mutational load associated with these genomic regions can be mitigated through marker-assisted selection.     

Comparison of the genetic determinism of two key phenological traits,flowering and maturity dates,in three Prunus species: peach,apricot and sweet cherry

The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3–8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.