Consensus Map Research Articles

Deciphering genetic mechanisms of Al toxicity tolerance through meta-QTL analysis in rice (Oryza sativa L.)

Rice is known for its tolerance to high aluminum (Al) concentrations in soil. However, the precise genetic and physiological mechanisms are yet to be fully understood. Recent research has identified several candidate genes (CGs) and quantitative trait loci (QTLs) associated with Al toxicity tolerance in rice. Nevertheless, many more QTLs/genes are yet to be precisely mapped. We employed meta-QTL (M-QTL) analysis, integrating 12 independent mapping studies and 5 Genome-Wide Association Studies (GWAS). The meta-analysis identified 53 M-QTLs from 157 projected QTLs, which were further narrowed down to 28 M-QTLs based on the number of overlapping QTLs on a consensus map. Gene identification through batch retrieval from the RAP database yielded 2,765 non-redundant genes within the 28 M-QTL regions. Comparison of M-QTL CGs with six expression datasets associated with Al toxicity tolerance in rice resulted in the identification of 219 CGs with significant differential expression. Notably, 34 CGs were identified to be common across at least 2 studies. Further downstream analyses of CGs revealed the presence of cis-regulatory elements, transcription factors, and transporter proteins related to the Al toxicity tolerance response. Additionally, we analyzed the expression patterns of the four CGs, namely NRT2.3, ALMT4, MT1, and MTP11, which showed significant upregulation in the Al toxicity-tolerant rice genotype, Anjali. Conversely, in the sensitive genotype Swarna, only NRT2.3 exhibited upregulation, while ALMT4, MT1, and MTP11 were downregulated. Our study highlights significant meta-regions that hold the potential for improving rice genotypes for enhanced tolerance to Al toxicity in acidic soils.

Myrmecophaga tridactyla (Linnaeus, 1758) subfossils from Abismo Anhumas, Bonito/MS, Brazil: Morphology, isotopic habitat (δ13C, δ18O), radiocarbon dating, biogeography and human impact on the species conservation in Brazil

ABSTRACTMyrmecophaga tridactyla Linnaeus, 1758 is the largest extant anteater, being distributed in most biomes from southern Central America and northern South America. Herein, we analyzed cranial and postcranial elements of three partial skeletons of M. tridactyla found submerged in Abismo Anhumas cave (Bonito, Mato Grosso do Sul, Brazil). The bones collected were the skull (LEG 2598), left humerus (LEG 2601), ungueal phalanx (LEG 2602), and lumbar vertebrae (LEG 2599; LEG 2600). Radiocarbon dating and isotope analyses indicate that these animals lived between 360 and 560 cal a BP in an arboreal to open savanna habitat associated with the Cerrado, a Seasonal Dry Forest. Radiocarbon‐dated oxygen isotopes are possibly in agreement with dated oxygen isotopes found in stalagmites, suggesting a wet period between 442–364 cal a BP in the region. Finally, we created paleo‐species distribution models, which allowed the generation of a consensus map showing a historically stable area between 21 and 6 ka for this species. Currently, more than 50% of this area has been destroyed by human activity.

Consensus QTL map deciphered genes and pathways regulating tolerance to post‐flowering diseases in maize

AbstractPost‐flowering diseases (PFDs), such as ear rot, stalk rot and smut, affect maize yield and quality by damaging the reproductive organs, stalks and seeds. We hypothesized that quantitative trait loci (QTL) associated with different PFDs colocalize and share similar defence mechanisms. Hence, to find a stable consensus meta‐QTL (MQTL) for single or multiple PFDs, MQTL analysis was performed. QTL conferring resistance to PFD reported in 31 independent studies were collated to develop a consensus map. As many as 49 MQTL conferring PFD resistance were projected using appropriate algorithms. Most MQTL regions encompass genes encoding a wide range of defence‐related proteins. MQTL1.1 and MQTL10.5 included QTL/genes for resistance to all PFDs, which supported our hypothesis. Candidate genes for PFDs in MQTL7.1 were associated with pathogenesis‐related 1 protein and mitogen‐activated protein kinase (MAPK) signalling. MQTL5.2 encompassed chalcone flavanone isomerase and cinnamoyl coenzyme A (CoA) reductase genes involved in flavonoid and phenylpropanoid biosynthesis, respectively. Furthermore, MQTL10.4 was found to harbour genes encoding E3 ubiquitin ligase, WRKY‐TF11, calcium‐binding domains and zinc finger motifs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis reiterated the role of genes within MQTL7.1 in the MAPK signalling pathway, phytohormone signal transduction and plant–pathogen interaction. Hence, we propose that these genes are potential candidates for PFD resistance. Furthermore, 75% of the genes within the MQTL showed orthology with sorghum and rice, indicating that these genes were conserved across species. The role of 27 MQTL, including the six most significant MQTL, was confirmed with reported genome‐wide association study (GWAS) results. Thus, the hotspots associated with PFDs identified in our study could be reliably used in marker‐assisted breeding for PFD resistance.

QTL Mapping of Melampsora Leaf Rust Resistance and Yield Component Traits in the SalixF1 Hybrid Common Parent Population

ABSTRACTThe first step in trait introgression is to identify and assess novel sources of variation. For shrub willow (Salix) breeders, there is an abundance of understudied species within a genus that readily hybridizes. Breeding targets in shrub willow center on traits contributing to biomass yield for bioenergy. These include stem biomass, insect and pathogen resistance, and leaf architecture traits. More specifically, breeding for durable resistance to willow leaf rust (Melampsora spp.) is of particular importance as the pathogen can significantly reduce biomass yields in commercial production. The Salix F1 hybrid common parent population (Salix F1 HCP) was created to characterize the variation among eight species‐hybrid families and map QTL for targeted traits. A female and male S. purpurea were used as common parents in crosses made to male S. suchowensis, S. viminalis, S. koriyanagi, and S. udensis and female S. viminalis, S. integra, S. suchowensis to produce eight families that were planted in field trials at Cornell AgriTech in Geneva, NY and phenotyped. Using 16 previously described parental backcross linkage maps and two newly generated S. purpurea consensus maps, we identified 215 QTL across all eight families and in every parent. These included 15 leaf rust severity, 61 herbivory, 65 leaf architecture, and 74 yield component QTL, resulting in 50 unique overlapping regions within the population. These genetic loci serve as an important foundation for future shrub willow breeding, and each interspecific family was identified as a novel source of useful alleles for trait introgression into high yielding cultivars.

A Multi-Dimensional Approach to Map Disease Relationships Challenges Classical Disease Views.

The categorization of human diseases is mainly based on the affected organ system and phenotypic characteristics. This is limiting the view to the pathological manifestations, while it neglects mechanistic relationships that are crucial to develop therapeutic strategies. This work aims to advance the understanding of diseases and their relatedness beyond traditional phenotypic views. Hence, the similarity among 502 diseases is mapped using six different data dimensions encompassing molecular, clinical, and pharmacological information retrieved from public sources. Multiple distance measures and multi-view clustering are used to assess the patterns of disease relatedness. The integration of all six dimensions into a consensus map of disease relationships reveals a divergent disease view from the International Classification of Diseases (ICD), emphasizing novel insights offered by a multi-view disease map. Disease features such as genes, pathways, and chemicals that are enriched in distinct disease groups are identified. Finally, an evaluation of the top similar diseases of three candidate diseases common in the Western population shows concordance with known epidemiological associations and reveals rare features shared between Type 2 diabetes (T2D) and Alzheimer's disease. A revision of disease relationships holds promise for facilitating the reconstruction of comorbidity patterns, repurposing drugs, and advancing drug discovery in the future.

Exploring the genetic architecture of powdery mildew resistance in wheat through QTL meta-analysis.

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, poses a significant threat to wheat production, necessitating the development of genetically resistant varieties for long-term control. Therefore, exploring genetic architecture of PM in wheat to uncover important genomic regions is an important area of wheat research. In recent years, the utilization of meta-QTL (MQTL) analysis has gained prominence as an essential tool for unraveling the complex genetic architecture underlying complex quantitative traits. The aim of this research was to conduct a QTL meta-analysis to pinpoint the specific genomic regions in wheat responsible for governing PM resistance. This study integrated 222 QTLs from 33 linkage-based studies using a consensus map with 54,672 markers. The analysis revealed 39 MQTLs, refined to 9 high-confidence MQTLs (hcMQTLs) with confidence intervals of 0.49 to 12.94 cM. The MQTLs had an average physical interval of 41.00 Mb, ranging from 0.000048 Mb to 380.71 Mb per MQTL. Importantly, 18 MQTLs co-localized with known resistance genes like Pm2, Pm3, Pm8, Pm21, Pm38, and Pm41. The study identified 256 gene models within hcMQTLs, providing potential targets for marker-assisted breeding and genomic prediction programs to enhance PM resistance. These MQTLs would serve as a foundation for fine mapping, gene isolation, and functional genomics studies, facilitating a deeper understanding of molecular mechanisms. The identification of candidate genes opens up exciting possibilities for the development of PM-resistant wheat varieties after validation.

Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat

In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1–57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.

Genome-wide screening of meta-QTL and candidate genes controlling yield and yield-related traits in barley (Hordeum vulgare L.).

Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001-2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder's MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley.

Meta QTL analysis for dissecting abiotic stress tolerance in chickpea

BackgroundChickpea is prone to many abiotic stresses such as heat, drought, salinity, etc. which cause severe loss in yield. Tolerance towards these stresses is quantitative in nature and many studies have been done to map the loci influencing these traits in different populations using different markers. This study is an attempt to meta-analyse those reported loci projected over a high-density consensus map to provide a more accurate information on the regions influencing heat, drought, cold and salinity tolerance in chickpea.ResultsA meta-analysis of QTL reported to be responsible for tolerance to drought, heat, cold and salinity stress tolerance in chickpeas was done. A total of 1512 QTL responsible for the concerned abiotic stress tolerance were collected from literature, of which 1189 were projected on a chickpea consensus genetic map. The QTL meta-analysis predicted 59 MQTL spread over all 8 chromosomes, responsible for these 4 kinds of abiotic stress tolerance in chickpea. The physical locations of 23 MQTL were validated by various marker-trait associations and genome-wide association studies. Out of these reported MQTL, CaMQAST1.1, CaMQAST4.1, CaMQAST4.4, CaMQAST7.8, and CaMQAST8.2 were suggested to be useful for different breeding approaches as they were responsible for high per cent variance explained (PVE), had small intervals and encompassed a large number of originally reported QTL. Many putative candidate genes that might be responsible for directly or indirectly conferring abiotic stress tolerance were identified in the region covered by 4 major MQTL- CaMQAST1.1, CaMQAST4.4, CaMQAST7.7, and CaMQAST6.4, such as heat shock proteins, auxin and gibberellin response factors, etc.ConclusionThe results of this study should be useful for the breeders and researchers to develop new chickpea varieties which are tolerant to drought, heat, cold, and salinity stresses.

A consensus map for Ladakh’s development as potential geotourism destination: key drivers

PurposeGiven the prevalence of protecting geoheritage tourism sites, Ladakh has enormous potential. However, Ladakh’s potential and developments in its growth as a geotourism destination have received scant consideration. As such, this paper aims to explore Ladakh’s key drivers as a potential geotourism destination through cognitive dissonance and protection motivation theories.Design/methodology/approachThis paper conducted in-depth interviews with 86 geoscientists and tourism professionals to assess Ladakh’s potential as a geotourism destination. This paper used a qualitative approach to congregate four constructs based on the image difference of the consensus map.FindingsBecause of the interviewees’ heterogeneity and uniqueness, meaningful constructs in the consensus were included for each figure and cloud words. This paper concluded that four drivers are the main forces behind geotourism development.Originality/valueThis paper explores the drivers – geotourism services, legislative requirements, experiential geotourism and SPARC (scientific, preservation, aesthetic, recreational, cultural) values – affecting geotourism in Ladakh. It is feasible to lessen the negative effects of overtourism and make sure that Ladakh’s distinctive nature is preserved for future generations by implementing sustainable tourism practices.

The methodology of constructing a high-density grapevine consensus map: integrating data from three mapping populations using the Vitis18K SNP chip with a reference genome sequence

The methodology of constructing a high-density grapevine consensus map: integrating data from three mapping populations using the <i>Vitis</i>18K SNP chip with a reference genome sequence

Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis.

Improving barley grain quality is a major goal in barley breeding. In this study, a total of 35 papers focusing on quantitative trait loci (QTLs) mapping for barley quality traits published since 2000 were collected. Among the 454 QTLs identified in these studies, 349 of them were mapped onto high-density consensus maps, which were used for QTL meta-analysis. Through QTL meta-analysis, the initial QTLs were integrated into 41 meta-QTLs (MQTLs) with an average confidence interval (CI) of 1. 66 cM, which is 88.9% narrower than that of the initial QTLs. Among the 41 identified MQTLs, 25 were subsequently validated in publications using genome-wide association study (GWAS). From these 25 validated MQTLs, ten breeder's MQTLs were selected. Synteny analysis comparing barley and wheat MQTLs revealed orthologous relationships between eight breeder's MQTLs and 45 wheat MQTLs. Additionally, 17 barley homologs associated with rice quality traits were identified within the regions of the breeder's MQTLs through comparative analysis. The findings of this study provide valuable insights for molecular marker-assisted breeding and the identification of candidate genes related to quality traits in barley.

A Fuzzy Entropy-Based Group Consensus Measure for Financial Investments

This study presents a novel, fuzzy entropy-based approach to the measurement of consensus in group decision making. Here, the basic assumption is that the decision inputs are the ‘yes’ or ‘no’ votes of group members on a financial investment that has a particular expected rate of return. In this paper, using a class of fuzzy entropies, a novel consensus measure satisfying reasonable requirements is introduced for a case where the decision inputs are dichotomous variables. It is also shown here that some existing consensus measures are just special cases of the proposed fuzzy entropy-based consensus measure when the input variables are dichotomous. Next, the so-called group consensus map for financial investments is presented. It is demonstrated that this construction can be used to characterize the level of consensus among the members of a group concerning financial investments as a function of the expected rate of return. Moreover, it is described how a consensus map can be constructed from empirical data and how this map is connected with behavioral economics.

Genomic regions involved in the control of 1,000-kernel weight in wild relative-derived populations of durum wheat

Terminal drought is one of the most common and devastating climatic stress factors affecting durum wheat (Triticum durum Desf.) production worldwide. The wild relatives of this crop are deemed a vast potential source of useful alleles to adapt to this stress. A nested association mapping (NAM) panel was generated using as a recurrent parent the Moroccan variety ‘Nachit’ derived from Triticum dicoccoides and known for its large grain size. This was recombined to three top-performing lines derived from T. dicoccoides, T. araraticum, and Aegilops speltoides, for a total of 426 inbred progenies. This NAM was evaluated across eight environments (Syria, Lebanon, and Morocco) experiencing different degrees of terminal moisture stress over two crop seasons. Our results showed that drought stress caused on average 41% loss in yield and that 1,000-kernel weight (TKW) was the most important trait for adaptation to it. Genotyping with the 25K TraitGenetics array resulted in a consensus map of 1,678 polymorphic SNPs, spanning 1,723 cM aligned to the reference ‘Svevo’ genome assembly. Kinship distinguished the progenies in three clades matching the parent of origin. A total of 18 stable quantitative trait loci (QTLs) were identified as controlling various traits but independent from flowering time. The most significant genomic regions were named Q.ICD.NAM-04, Q.ICD.NAM-14, and Q.ICD.NAM-16. Allelic investigation in a second germplasm panel confirmed that carrying the positive allele at all three loci produced an average TKW advantage of 25.6% when field-tested under drought conditions. The underlying SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and successfully validated in a third germplasm set, where they explained up to 19% of phenotypic variation for TKW under moisture stress. These findings confirm the identification of critical loci for drought adaptation derived from wild relatives that can now be readily exploited via molecular breeding.

Surveying the genomic landscape of silage-quality traits in maize (Zea mays L.)

Despite the longstanding importance of silage as a critical feed source for ruminants, its quality improvement has been largely overlooked. Although numerous quantitative trait loci (QTL) and genes affecting silage quality in maize have been reported, only a few have been effectively incorporated into breeding programs. Addressing this gap, the present study undertook a comprehensive meta-QTL (MQTL) analysis involving 523 QTL associated with silage-quality traits collected from 14 published studies. Of the 523 QTL, 405 were projected onto a consensus map comprising 62,424 genetic markers, resulting in the identification of 60 MQTL and eight singletons. The average confidence interval (CI) of the MQTL was 3.9-fold smaller than that of the source QTL. Nine of the 60 identified MQTL were classified as breeder’s MQTL owing to their small CIs, involvement of more QTL, and large contribution to phenotypic variation. One-third of the MQTL co-localized with DNA marker-trait associations identified in previous genome-wide association mapping studies. A set of 78 high-confidence candidate genes influencing silage quality were identified in the MQTL regions. These genes and associated markers may advance marker-assisted breeding for maize silage quality.

Berry texture QTL and candidate gene analysis in grape (Vitis vinifera L.).

Berry texture is a noteworthy economic trait for grape; however, the genetic bases and the complex gene expression and regulatory mechanism for the diverse changes in berry texture are still poorly understood. In this study, the results suggest that it is difficult to obtain high-mesocarp firmness (MesF) and high-pericarp puncture hardness (PPH) grape cultivars with high pericarp brittleness (PerB). The high-density linkage map was constructed using whole-genome resequencing based on 151 F1 individuals originating from intraspecific hybridization between the firm-flesh cultivar 'Red Globe' and soft-flesh cultivar 'Muscat Hamburg'. The total length of the consensus map was 1613.17cM, with a mean genetic distance between adjacent bin markers of 0.59cM. Twenty-seven quantitative trait loci (QTLs) for berry MesF, PPH, and PerB were identified in linkage groups (LGs) 1, 3, 4, 6, 8, 9, 10, 11, 14, 16, and 17, including twelve QTLs that were firstly detected in LGs 6, 11, and 14. Fourteen promising candidate genes were identified from the stable QTL regions in LGs 10, 11, 14, and 17. In particular, VvWARK2 and VvWARK8 refer to chromosome 17 and are two promising candidate genes for MesF and PPH, as the VvWARK8 gene may increase pectin residue binding with WARK for high berry firmness maintenance and the allele for VvWARK2 carrying the 'CC' and 'GA' genotypes at Chr17:1836764 and Chr17:1836770 may be associated with non-hard texture grape cultivars. In addition, real-time quantitative polymerase chain reaction (RT-qPCR) verification revealed that the promising candidate transcription factor genes VvMYB4-like, VvERF113, VvWRKY31, VvWRKY1, and VvNAC83 may regulate cell wall metabolism candidate gene expression for grape berry texture changes.

Predicting future conservation areas while avoiding sympatry in two alpine amphibians severely threatened by climate change

Climate change will cause important declines in environmental suitability, especially when living at high elevations. The critically endangered Salamandra lanzai from the Alps may be severely exposed to future climate change effects and its suitable climate niche may shrink or shift. Another Alpine salamander (S. atra) is present in the region, which in case of spatial overlap may represent a risk for S. lanzai. It is urgent to estimate the effect of future climate change on these species and identify priority areas for conservation while preventing their sympatry. With a species distribution modelling (SDM) approach, we projected the current and future climate suitability of both salamander species. We accounted for uncertainty related to the methods (model replicates) and climate projections (data source, global circulation model and scenario) to provide a consensus map for practitioners. This map also takes into account potential sympatry with S. atra by penalizing the suitability scores of S. lanzai by the scores of S. atra. We predict a severe effect of climate change on both species distributions. Most of the current habitats are projected to become largely unsuitable by 2070, regardless of the climatology and scenario. We identified important spatial disagreements between projections based on different data sources, mostly due to precipitation projections and daily temperature variation. This highlights the need to account for multiple climatologies in mountainous environments. The habitat of both species is highly fragmented, which is expected to limit distributional shifts through natural dispersion. We suggest to explore the possibility of translocation for the most threatened populations and simultaneously develop captive breeding programs. Biotic interactions are rarely accounted for in SDMs, and we encourage the documentation of species with similar ecological requirements to improve the relevance of SDMs for future conservation planning.

Mapping and chronological classification of marine terraces along the southern side of the Sibari Plain (northern Calabria, Italy) by means of digital and analogue tools

ABSTRACT We study the marine terraces of the southern side of the Sibari Plain in Northern Calabria (Italy) through the use of traditional and quantitative analyses of the Digital Terrain Model (DTM). The main aim of the present work consists in the extensive use of GIS tools that were never used before in the area, and in checking the applicability of this procedure. The terraced surfaces identified using photo interpretation and those recognized semi-automatically through the GIS tools were compared to finally produce a consensus map. In the final map, we identified 272 terraced surfaces and 62 morphological features associated with inner margins (i.e. paleoshorelines). The main map shows a well-developed flight of seven orders of marine terraces with elevation ranging from 45 to 360 m asl and age ranging from Marine Isotope Stage (MIS) 5a to 11.

A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.).

Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice.

Mapping of quantitative trait loci for growth traits around the first overwintering period in Songpu mirror carp (Cyprinus carpio L.) cultured in Northeast China

QTL mapping studies of growth traits based on high-density linkage maps in Northeast China has great significance for local enterprises in achieving MAS and improving the selection accuracy of parent fish. Here, we constructed a high-density genetic linkage map with 11,445 single nucleotide polymorphism (SNP) markers in a full-sib F1 family consisting of 120 progenies in Songpu mirror carp (Cyprinus carpio) reared in Northeast China. The consensus map covered 5471.93 centimorgans (cM) across the 50 linkage groups with an average resolution of 0.54 cM. Around the first overwintering period, a total of 15 QTLs for growth traits were identified on five LGs (LG7, LG8, LG14, LG30, and LG41). All of them were responsible for body weight (BW) at both 150 (before overwintering) and 350 (after overwintering) days, explaining 9.8–17.9 % of the phenotypic variation (PV). Two major-effect QTLs were detected on LG30, which explained 16.5 % and 16.4 % (qTL9–30), and 15.8 % and 17.9 % (qTL10–30) of the PV at 150 and 350 days, respectively. In addition, 15 loci were identified for 4 growth traits other than BW at both time points, including 6 loci for body length (BL), 7 loci for body height (BH), 3 loci for body thickness (BT) and 5 loci for head length (HL). These loci explained PV ranging from 15.9 % to 21.2 % for BL, 9.3–19.6 % for BH, 9.6–15.5 % for BT, and 10.6–18.1 % for HL. Nine candidate genes (IGF1b, LEPb, PACAP1a, GHSR1a, PPSS2, IRS1, APOAIb, IRS2b and ADSS1) were identified, five of which were directly related to growth hormone (GH), including IGF1b, PACAP1a, GHSR1a, PPSS2 and IRS1. Notably, three genes (GHSR1a, PPSS2 and IRS1) were derived from two major-effect QTLs (qTL9–30 and qTL10–30). In conclusion, these novel findings may shed light on early selection of growth traits of common carp cultured in Northeast China and other relatively high-latitude regions.