Common Quantitative Trait Loci Research Articles

Identification of QTLs for rice flower opening time in two environments

Flower opening time (FT) is a critical factor for seed production in hybrid rice. To unravel the genetic basis of FT, a recombinant inbred (RI) line population including 184 lines was developed from the cross between a japonica variety Nipponbare and an early FT mutant (eft). A genetic linkage map was constructed using 70 SSR and 123 InDel markers, covering a total length of 1753.3 cM of the genome. The FT of both parents and RI lines was measured by the traditional grading scale method and a new time-interval method in two environments, i.e., Hainan (HN) and Hangzhou (HZ). A total of seven FT-related quantitative trait loci (QTLs) distributing on 4 chromosomes were detected in HN and HZ. qFT1b and qFT12 could be detected in both environments. The time-interval FT in Hangzhou allowed us to detect one more QTL (qFT-9) than the grading scale method. qFT1a is a major QTL explaining more than 60% of the total phenotypic variations in FT. Although FT had a positive correlation with heading date in Hangzhou (r = 0.16), no common QTL was detected for them, suggesting that FT and heading date are under different genetic controls. These discoveries may help to understand the genetics of flower opening time in rice and be useful for breeding early FT rice to facilitate hybrid seed production in the near future.

Dissection of the genetic architecture for tassel branch number by QTL analysis in two related populations in maize

Tassel branch number (TBN) is the principal component of maize tassel inflorescence architecture and is a typical quantitative trait controlled by multiple genes. The main objective of this research was to detect quantitative trait loci (QTLs) for TBN. The maize inbred line SICAU1212 was used as the common parent to develop BC1S1 and recombinant inbred line (RIL) populations with inbred lines 3237 and B73, respectively. The two related populations consisted of 123 and 238 lines, respectively. Each population was grown and phenotyped for TBN in two environments. Eleven QTLs were detected in the BC1S1 population, located on chromosomes 2, 3, 5, and 7, accounted for 4.45–26.58% of the phenotypic variation. Two QTLs (qB11Jtbn2-1, qB12Ctbn2-1, qBJtbn2-1; q11JBtbn5-1, qB12Ctbn5-1, qBJtbn5-1) that accounted for more than 10% of the phenotypic variation were identified. Three QTLs located on chromosomes 2, 3 and 5, exhibited stable expression in the two environments. Ten QTLs were detected in the RIL population, located on chromosomes 2, 3, 5, 8, and 10, accounted for 2.69–13.58% of the TBN variation. One QTL (qR14Dtbn2-2) explained >10% of the phenotypic variation. One common QTL (qB12Ctbn2-2, qR14Dtbn2-2, qRJtbn2-2) was detected between the two related populations. Three pairs of epistatic effects were identified between two loci with or without additive effects and accounted for 1.19–4.26% of the phenotypic variance. These results demonstrated that TBN variation was mainly caused by major effects, minor effects and slightly modified by epistatic effects. Thus, identification of QTL for TBN may help elucidate the genetic basis of TBN and also facilitate map-based cloning and marker-assisted selection (MAS) in maize breeding programs.

Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation.

Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years.

Background and Aims Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype–phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. Methods A hybrid Salix viminalis × (S. viminalis × Salix schwerinii) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. Key Results Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. Conclusions The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis × S. schwerinii populations.

Genetic Architecture of Resistance to Alternaria brassicae in Arabidopsis thaliana: QTL Mapping Reveals Two Major Resistance-Conferring Loci.

Alternaria brassicae, a necrotrophic fungal pathogen, causes Alternaria blight, one of the most important diseases of oleiferous Brassica crops. The current study utilized Arabidopsis as a model to decipher the genetic architecture of defense against A. brassicae. Significant phenotypic variation that was largely genetically determined was observed among Arabidopsis accessions in response to pathogen challenge. Three biparental mapping populations were developed from three resistant accessions viz. CIBC-5, Ei-2, and Cvi-0 and two susceptible accessions – Gre-0 and Zdr-1 (commonly crossed to CIBC-5 and Ei-2). A total of six quantitative trait locus (QTLs) governing resistance to A. brassicae were identified, five of which were population-specific while one QTL was common between all the three mapping populations. Interestingly, the common QTL had varying phenotypic contributions in different populations, which can be attributed to the genetic background of the parental accessions. The presence of both common and population-specific QTLs indicate that resistance to A. brassicae is quantitative, and that different genes may mediate resistance to the pathogen in different accessions. Two of the QTLs had moderate-to-large effects, one of which explained nearly 50% of the variation. The large effect QTLs may therefore contain genes that could play a significant role in conferring resistance even in heterologous hosts.

Common Bacterial Blight Resistance QTL BC420 and SU91 Effect on Seed Yield, Seed Weight, and Canning Quality in Dry Bean

Common bacterial blight (CBB) disease limits dry bean (Phaseolus vulgaris L.) production worldwide. Resistance quantitative trait loci (QTL) from tepary bean (Phaseolus acutifolius A. Gray) have been used to develop dry bean lines with high levels of CBB resistance. This study examines the effects that two QTL from tepary bean BC420 (B) on chromosome Pv06 and SU91 (S) on Pv08 have on agronomic (seed yield and seed weight) and canning quality traits (water uptake, percentage washed drained weight [PWDWT], texture, and visual appearance). Sixteen small white dry bean near‐isogenic lines, representing four homozygous genotypes for the BC420 and SU91 QTL BBSS, bbSS, BBss, and bbss, the donor resistant parent Teebus‐BC5 (BBSS), and the recurrent susceptible parent ‘Teebus’ (bbss) were tested in replicated, inoculated and non‐inoculated field plots across five environments in South Africa. Plots were inoculated with a mixture of Xanthomonas axonopodis pv. phaseoli and X. fuscans sbsp. fuscans isolates. The BC420 and SU91 QTL did not cause a yield penalty in non‐inoculated plots in environments with low to no disease. SU91 provided yield protection under severe disease pressure, and both QTL in combination reduced disease severity score under moderate to high disease pressure. Seed weight was maintained in lines with the QTL under severe to moderate pressure and was unaffected by the QTL in low‐ to no‐disease environments. Water uptake was significantly reduced in genotypes with BC420 (BBSS, BBss) and likely influenced traits measured subsequently: lower PWDWT, firmer texture, and less attractive visual appearance, which contributed to a reduced canning quality overall. Deployment of BC420 and SU91 QTL can be safely recommended for control of CBB, as no agronomic penalty was observed in CBB‐free conditions, but canning quality should be closely monitored in lines with BC420 QTL.

Detection of epistatic and environmental interaction QTLs for leaf orientation‐related traits in maize

AbstractLeaf architecture traits in maize are quantitative and have been studied by quantitative trait loci (QTLs) mapping. However, additional QTLs for these traits require mapping and the interactions between mapped QTLs require studying because of the complicated genetic nature of these traits. To detect common QTLs and to find new ones, we investigated the maize traits of leaf angle, leaf flagging‐point length, leaf length and leaf orientation value using a set of recombinant inbred line populations and single nucleotide polymorphism markers. In total, 19 QTLs contributed 4.13–13.52% of the phenotypic effects to the corresponding traits that were mapped, and their candidate genes are provided. Common and major QTLs have also been detected. All of the QTLs showed significant additive effects and non‐significant additive × environment effects in combined environments. The majority showed additive × additive epistasis effects and non‐significant QTL × environment effects under single environments. Common and major QTLs provided information for fine mapping and gene cloning, and SNP markers can be used for marker‐assisted selection breeding.

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits.

Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.

A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars.

Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield. Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling tiller angle using 529 diverse accessions of Oryza sativa including 295 indica and 156 japonica accessions in two environments. We identified 7 common quantitative trait loci (QTLs), including the previously reported major gene Tiller Angle Control 1 (TAC1), in the two environments, 10 and 13 unique QTLs in Hainan and Wuhan, respectively. More QTLs were identified in indica than in japonica, and three major QTLs (qTA3, qTA1b/DWARF2 (D2) and qTA9c/TAC1) were fixed in japonica but segregating in indica, which explained the wider variation observed in indica compared with that in japonica. No common QTLs were identified between the indica and japonica subpopulations. Mutant analysis for the candidate gene of qTA3 on chromosome 3 indicated a novel gene, Tiller Angle Control 3 (TAC3), encoding a conserved hypothetical protein controlling tiller angle. TAC3 is preferentially expressed in the tiller base. The ebisu dwarf (d2) mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A nucleotide diversity analysis revealed that TAC3, D2 and TAC1 have been subjected to selection during japonica domestication. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1, which may be used for breeding plants with an ideal architecture. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3 together with TAC1, D2, and other newly identified genes in this study that controls tiller angle in rice cultivars.

Genetic Determinism of Sensitivity to Corynespora cassiicola Exudates in Rubber Tree (Hevea brasiliensis).

An indirect phenotyping method was developed in order to estimate the susceptibility of rubber tree clonal varieties to Corynespora Leaf Fall (CLF) disease caused by the ascomycete Corynespora cassiicola. This method consists in quantifying the impact of fungal exudates on detached leaves by measuring the induced electrolyte leakage (EL%). The tested exudates were either crude culture filtrates from diverse C. cassiicola isolates or the purified cassiicolin (Cas1), a small secreted effector protein produced by the aggressive isolate CCP. The test was found to be quantitative, with the EL% response proportional to toxin concentration. For eight clones tested with two aggressive isolates, the EL% response to the filtrates positively correlated to the response induced by conidial inoculation. The toxicity test applied to 18 clones using 13 toxinic treatments evidenced an important variability among clones and treatments, with a significant additional clone x treatment interaction effect. A genetic linkage map was built using 306 microsatellite markers, from the F1 population of the PB260 x RRIM600 family. Phenotyping of the population for sensitivity to the purified Cas1 effector and to culture filtrates from seven C. cassiicola isolates revealed a polygenic determinism, with six QTL detected on five chromosomes and percentages of explained phenotypic variance varying from 11 to 17%. Two common QTL were identified for the CCP filtrate and the purified cassiicolin, suggesting that Cas1 may be the main effector of CCP filtrate toxicity. The CCP filtrate clearly contrasted with all other filtrates. The toxicity test based on Electrolyte Leakage Measurement offers the opportunity to assess the sensitivity of rubber genotypes to C. cassiicola exudates or purified effectors for genetic investigations and early selection, without risk of spreading the fungus in plantations. However, the power of this test for predicting field susceptibility of rubber clones to CLF will have to be further investigated.

Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat.

BackgroundPre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (QTL) have been reported for PHS resistance, and two of them on chromosome 3AS (TaPHS1) and 4A have been cloned.MethodsTo determine genetic architecture of PHS and GC and genetic relationships of the two traits, a genome-wide association study (GWAS) was conducted by evaluating a panel of 185 U.S. elite breeding lines and cultivars for sprouting rates of wheat spikes and GC in both greenhouse and field experiments. The panel was genotyped using the wheat 9K and 90K single nucleotide polymorphism (SNP) arrays.ResultsFour QTL for GC on four chromosomes and 12 QTL for PHS resistance on 10 chromosomes were identified in at least two experiments. QTL for PHS resistance showed varied effects under different environments, and those on chromosomes 3AS, 3AL, 3B, 4AL and 7A were the more frequently identified QTL. The common QTL for GC and PHS resistance were identified on the long arms of the chromosome 3A and 3D.ConclusionsWheat grain color is regulated by the three known genes on group 3 chromosomes and additional genes from other chromosomes. These grain color genes showed significant effects on PHS resistance in some environments. However, several other QTL that did not affect grain color also played a significant role on PHS resistance. Therefore, it is possible to breed PHS-resistant white wheat by pyramiding these non-color related QTL.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3148-6) contains supplementary material, which is available to authorized users.

Mapping QTLs associated with agronomic and physiological traits under terminal drought and heat stress conditions in wheat (Triticum aestivum L.).

Wheat crops frequently experience a combination of abiotic stresses in the field, but most quantitative trait loci (QTL) studies have focused on the identification of QTLs for traits under single stress field conditions. A recombinant inbred line (RIL) population derived from SeriM82 × Babax was used to map QTLs under well-irrigated, heat, drought, and a combination of heat and drought stress conditions in two years. A total of 477 DNA markers were used to construct linkage groups that covered 1619.6 cM of the genome, with an average distance of 3.39 cM between adjacent markers. Moderate to relatively high heritability estimates (0.60-0.70) were observed for plant height (PHE), grain yield (YLD), and grain per square meter (GM2). The most important QTLs for days to heading (DHE), thousand grain weight (TGW), and YLD were detected on chromosomes 1B, 1D-a, and 7D-b. The prominent QTLs related to canopy temperature were on 3B. Results showed that common QTLs for DHE, YLD, and TGW on 7D-b were validated in heat and drought trials. Three QTLs for chlorophyll content in SPAD unit (on 1A/6B), leaf rolling (ROL) (on 3B/4A), and GM2 (on 1B/7D-b) showed significant epistasis × environment interaction. Six heat- or drought-specific QTLs (linked to 7D-acc/cat-10, 1B-agc/cta-9, 1A-aag/cta-8, 4A-acg/cta-3, 1B-aca/caa-3, and 1B-agc/cta-9 for day to maturity (DMA), SPAD, spikelet compactness (SCOM), TGW, GM2, and GM2, respectively) were stable and validated over two years. The major DHE QTL linked to 7D-acc/cat-10, with no QTL × environment (QE) interaction increased TGW and YLD. This QTL (5.68 ≤ LOD ≤ 10.5) explained up to 19.6% variation in YLD in drought, heat, and combined stress trials. This marker as a candidate could be used for verification in other populations and identifying superior allelic variations in wheat cultivars or its wild progenitors to increase the efficiency of selection of high yielding lines adapted to end-season heat and drought stress conditions.

Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice.

Rice is a short-day plant. Short-day length promotes heading, and long-day length suppresses heading. Many studies have evaluated rice heading in field conditions in which some individuals in the population were exposed to various day lengths, including short and long days, prior to a growth phase transition. In this study, we investigated heading date under natural short-day conditions (SD) and long-day conditions (LD) for 100s of accessions and separately conducted genome-wide association studies within indica and japonica subpopulations. Under LD, three and four quantitative trait loci (QTLs) were identified in indica and japonica subpopulations, respectively, two of which were less than 80 kb from the known genes Hd17 and Ghd7. But no common QTLs were detected in both subpopulations. Under SD, six QTLs were detected in indica, three of which were less than 80 kb from the known heading date genes Ghd7, Ehd1, and RCN1. But no QTLs were detected in japonica subpopulation. qHd3 under SD and qHd4 under LD were two novel major QTLs, which deserve isolation in the future. Eleven known heading date genes were used to test the power of association mapping at the haplotype level. Hd17, Ghd7, Ehd1, and RCN1 were again detected at more significant level and three additional genes, Hd3a, OsMADS56, and Ghd7.1, were detected. However, of the detected seven genes, only one gene, Hd17, was commonly detected in both subpopulations and two genes, Ghd7 and Ghd7.1, were commonly detected in indica subpopulation under both conditions. Moreover, haplotype analysis identified favorable haplotypes of Ghd7 and OsMADS56 for breeding design. In conclusion, diverse heading date genes/QTLs between indica and japonica subpopulations responded to SD and LD, and haplotype-level association mapping was more powerful than SNP-level association in rice.

An Upper Bound for Accuracy of Prediction Using GBLUP.

This study aims at characterizing the asymptotic behavior of genomic prediction R2 as the size of the reference population increases for common or rare QTL alleles through simulations. Haplotypes derived from whole-genome sequence of 85 Caucasian individuals from the 1,000 Genomes Project were used to simulate random mating in a population of 10,000 individuals for at least 100 generations to create the LD structure in humans for a large number of individuals. To reduce computational demands, only SNPs within a 0.1M region of each of the first 5 chromosomes were used in simulations, and therefore, the total genome length simulated was 0.5M. When the genome length is 30M, to get the same genomic prediction R2 as with a 0.5M genome would require a reference population 60 fold larger. Three scenarios were considered varying in minor allele frequency distributions of markers and QTL, for h2 = 0.8 resembling height in humans. Total number of markers was 4,200 and QTL were 70 for each scenario. In this study, we considered the prediction accuracy in terms of an estimability problem, and thereby provided an upper bound for reliability of prediction, and thus, for prediction R2. Genomic prediction methods GBLUP, BayesB and BayesC were compared. Our results imply that for human height variable selection methods BayesB and BayesC applied to a 30M genome have no advantage over GBLUP when the size of reference population was small (<6,000 individuals), but are superior as more individuals are included in the reference population. All methods become asymptotically equivalent in terms of prediction R2, which approaches genomic heritability when the size of the reference population reaches 480,000 individuals.

Potential preadaptation to anthropogenic pollution: evidence from a common quantitative trait locus for zinc and cadmium tolerance in metallicolous and nonmetallicolous accessions of Arabidopsis halleri.

As a drastic environmental change, metal pollution may promote the rapid evolution of genetic adaptations contributing to metal tolerance. In Arabidopsis halleri, genetic bases of zinc (Zn) and cadmium (Cd) tolerance have been uncovered only in a metallicolous accession, although tolerance is species-wide. The genetic determinants of Zn and Cd tolerance in a nonmetallicolous accession were thus investigated for the first time. The genetic architecture of tolerance was investigated in a nonmetallicolous population (SK2) by using first backcross progeny obtained from crosses between SK2 and Arabidopsis lyrata petraea, a nonmetallophyte species. Only one significant and common quantitative trait locus (QTL) region was identified explaining 22.6% and 31.2% of the phenotypic variation for Zn and Cd tolerance, respectively. This QTL co-localized with HEAVY METAL ATPASE 4 (AhHMA4), which was previously validated as a determinant of Zn and Cd tolerance in a metallicolous accession. Triplication and high expression of HMA4 were confirmed in SK2. In contrast, gene duplication and high expression of METAL TOLERANT PROTEIN 1A (MTP1A), which was previously associated with Zn tolerance in a metallicolous accession, were not observed in SK2. Overall, the results support the role of HMA4 in tolerance capacities of A.halleri that may have pre-existed in nonmetallicolous populations before colonization of metal-polluted habitats. Preadaptation to metal-contaminated sites is thus discussed.

Genetic Mapping Reveals Broader Role of Vrn-H3 Gene in Root and Shoot Development beyond Heading in Barley.

The aim of the present study was to dissect the genetic inheritance and interplay of root, shoot and heading attributes for a better understanding of these traits in crop production. For this, we utilized quantitative trait loci (QTL) and candidate gene analysis approach using a second filial (F2) population originated from a cross between spring cultivar Cheri and wild barley accession ICB181160. The F2 population comprising 182 plants was phenotyped for root dry weight (RDW), root volume (RV), root length (RL) and shoot dry weight (SDW), tiller number per plant (TIL) and days to heading (HEA). In parallel, this population was genotyped using polymerase chain reaction (PCR) based cleaved amplified polymorphic sequence (CAPS) markers distributed across the whole genome. Marker by trait analysis revealed 16 QTL for root and shoot traits localized on chromosomes 1H, 3H, 4H, 5H and 7H. The strongest and a common QTL effect for root, shoot and heading traits was identified on chromosome 7H at the putative region of Vrn-H3 gene. Later, we have established PCR based gene specific marker HvVrnH3 revealing polymorphism for early heading Vrn-H3 allele in Cheri and late heading allele vrn-H3 in ICB181160. Genotyping of these alleles revealed a clear co-segregation of early heading Vrn-H3 allele with lower root and shoot attributes, while late heading vrn-H3 allele with more TIL and higher root biomass suggesting a primary insight on the function of Vrn-H3 gene beyond flowering. Genetic interactions of vernalization genes Vrn-H3 with Vrn-H2 and Vrn-H1 also suggested the major role of Vrn-H3 alleles in determining root and shoot trait variations in barley. We believe, these data provide an opportunity for further research to test a precise significance of early heading on yield components and root associated sustainability in crops like barley and wheat.

QTL mapping of grain yield and phosphorus efficiency in barley in a Mediterranean-like environment.

Key QTLs were identified for P efficiency in barley. Phosphorus efficiency and grain yield can be improved simultaneously in breeding. An important breeding goal for many crop species is improved phosphorus (P) efficiency. As in many other crops, selection for P efficient barley varieties has been slow because of inconsistent definitions of P efficiency and unknown genetic controls of P efficiency. We used two criteria to assess P efficiency in a doubled haploid Commander/Fleet population: P responsiveness (estimated as the deviation from the regression of yield with added P against yield with no added P treatment) and PUE (relative yield). Phosphorus responsiveness, PUE and grain yield were phenotyped at 0 and 30kgP/ha in five environments. Lines consistently responsive to 30kgP/ha across environments had the highest yield at the two P rates, and P responsiveness showed significantly higher broad sense heritability than PUE in the materials we studied. Genotyping of the population was subjected to a 9,000 single nucleotide polymorphism array and quantitative trait loci (QTLs) for P responsiveness were mapped with yield at 30kgP/ha, which are common QTLs for yield when P was not limiting growth. The largest QTL for P responsiveness was mapped to 7HL in 2years. PUE varied from 31 to 124% across environments and one of the QTLs for PUE was mapped with yield at 0kgP/ha. Our results demonstrate P responsiveness and grain yield can be improved simultaneously under high-input agricultural systems, but breeding for high PUE varieties may need to explore landrace or wild barley germplasm for low P tolerant alleles.

Multi-breed genome-wide association study reveals heterogeneous loci associated with loin eye area in pigs.

Numerous quantitative trait loci (QTL) for loin eye area had been identified by linkage mapping studies, but the lack of their precise position hinders their application in the pig breeding industry. To map QTL for loin eye area to a precise genomic region, we conducted a genome-wide association study (GWAS) using Illumina 60K PorcineSNP60 Beadchip in four swine populations: 819F2 pigs, 273 Laiwu pigs, 434 Sutai pigs, and 326 Erhualian pigs. In total, 26 single nucleotide polymorphisms (SNPs) deposited on seven chromosomes associated with loin eye area were identified, 11 of which surpassed the genome-wide significant threshold; of the 11 SNPs, seven located on SSC2 in F2 pigs and four located on SSC12 and SSC18 in Laiwu pigs. Of note, all of the identified QTL were breed specific and no common QTL was identified across the four populations in our study. These findings not only confirmed a previous QTL on SSC2 harboring the candidate gene insulin-like growth factor 2 (IGF2), but also identified some novel candidate genes, far upstream element binding protein 3 (FUBP3), myosin heavy chain (MYH) family, leucine-rich repeats and guanylate kinase domain containing (LRGUK). Our study will contribute to the further identification of the causal mutation underlying these QTL and improve our knowledge of the complex genetic architecture for loin eye area in pigs.

Identification of QTL for maize grain yield and kernel-related traits.

Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea mays L.) breeding practice. Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs). One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were used to genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW), 10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1) per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval between bnlg1893 and chr2- 236477 (chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simultaneously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved in chromosomal region at bin 2.03 was detected for HKW; no significant QTL × environment interactions were observed. These results provide the common QTLs and for marker-assisted breeding.

Genetic analysis of salt tolerance in a progeny derived from the citrus rootstocks Cleopatra mandarin and trifoliate orange

A total of 60 traits that could be related to salt tolerance were genetically analyzed using nucellar plants as repetitions of apomictic hybrids in a reference population derived from two common citrus rootstocks, Cleopatra mandarin (salt tolerant) and trifoliate orange (salt sensitive), in two experiments differing in duration (1 versus 3 years) [NaCl] (30 versus 25 mM) and environmental control (greenhouse versus screenhouse). In both experiments, the trifoliate parent always showed less aerial vegetative growth than Cleopatra, and under salinity, the trifoliate parent showed higher Na+ and Cl− leaf concentrations than the salt-tolerant parent. Salinity affected the relationships among traits, particularly those involving leaf water potential; leaf concentrations of Cl−, K+, B and Fe; and root [Na+]. Most traits showed heritabilities below 0.6, and their quantitative trait locus (QTL) analyses were carried out using three mapping procedures to obtain complementary genetic information on trait inheritance. A total of 98 QTLs were detected by interval mapping and multiple QTL mapping procedures. Fresh and dried weights of the leaf, studied in both experiments, showed common QTLs, remarking their repeatability. A cluster of QTLs governing plant vigour and leaf boron concentration pointed a genomic region in linkage group 3 as the most relevant one to improve salt tolerance using the Cleopatra parent as donor. Besides, a QTL genotype in linkage group 7, associated with the smallest leaf water potential and defoliation index under salinity, corresponded to the highest leaf [Na+] and the largest leaf area, suggesting the presence of a putative tissue salt tolerance QTL.