Genome-wide association analysis of seedling root development in maize (Zea mays L.)

Background

Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped.

Results

Utilizing both a general linear model and mixed linear model, a GWAS study was conducted identifying 268 marker trait associations (p ≤ 5.3×10^-7). Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions of previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is expressed in roots and shoots.

Conclusion

This study identifies putatively associated SNP markers associated with root traits at the seedling stage. Some SNPs were located within or near (<1 kb) gene models. These gene models identify possible candidate genes involved in root development at the seedling stage. These and respective linked or functional markers could be targets for breeders for marker assisted selection of seedling root traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1226-9) contains supplementary material, which is available to authorized users.     

Prediction of hybrid performance in maize using molecular markers and joint analyses of hybrids and parental inbreds

The identification of superior hybrids is important for the success of a hybrid breeding program. However, field evaluation of all possible crosses among inbred lines requires extremely large resources. Therefore, efforts have been made to predict hybrid performance (HP) by using field data of related genotypes and molecular markers. In the present study, the main objective was to assess the usefulness of pedigree information in combination with the covariance between general combining ability (GCA) and per se performance of parental lines for HP prediction. In addition, we compared the prediction efficiency of AFLP and SSR marker data, estimated marker effects separately for reciprocal allelic configurations (among heterotic groups) of heterozygous marker loci in hybrids, and imputed missing AFLP marker data for marker-based HP prediction. Unbalanced field data of 400 maize dent × flint hybrids from 9 factorials and of 79 inbred parents were subjected to joint analyses with mixed linear models. The inbreds were genotyped with 910 AFLP and 256 SSR markers. Efficiency of prediction (R ²) was estimated by cross-validation for hybrids having no or one parent evaluated in testcrosses. Best linear unbiased prediction of GCA and specific combining ability resulted in the highest efficiencies for HP prediction for both traits (R ² = 0.6–0.9), if pedigree and line per se data were used. However, without such data, HP for grain yield was more efficiently predicted using molecular markers. The additional modifications of the marker-based approaches had no clear effect. Our study showed the high potential of joint analyses of hybrids and parental inbred lines for the prediction of performance of untested hybrids.     

Identification of Diploid <Emphasis Type="Italic">Stylosanthes seabrana</Emphasis> Accessions from Existing Germplasm of <Emphasis Type="Italic">S. scabra</Emphasis> Utilizing Genome-Specific STS Markers and Flow Cytometry,and Their Molecular Characterization

Stylosanthes seabrana (Maass and ‘t Mannetje) (2n = 2x = 20), commonly known as Caatinga stylo, is an important tropical perennial forage legume. In nature, it largely co-exist with S. scabra, an allotetraploid (2n = 4x = 40) species, sharing a very high similarity for morphological traits like growth habit, perenniality, fruit shape and presence of small appendage at the base of the pod or loment. This makes the two species difficult to distinguish morphologically, leading to chances of contamination in respective germplasm collections. In present study, 10 S. seabrana accessions were discovered from the existing global germplasm stock of S. scabra represented by 48 diverse collections, utilizing sequence-tagged-sites (STS) genome-specific markers. All the newly identified S. seabrana accessions displayed STS phenotypes of typical diploid species. Earlier reports have conclusively indicated S. seabrana and S. viscosa as two diploid progenitors of allotetraploid S. scabra. With primer pairs SHST3F3/R3, all putative S. seabrana yielded single band of ~550 bp and S. viscosa of ~870 bp whereas both of these bands were observed in allotetraploid S. scabra. Since SHST3F3/R3 primer pairs are known to amplify single or no band with diploid and two bands with tetraploid species, the amplification patterns corroborated that all newly identified S. seabrana lines were diploid in nature. Flow cytometric measurement of DNA content of the species, along with distinguishing morphological traits such as flowering time and seedling vigour, which significantly differ from S. scabra, confirmed all identified lines as S. seabrana. These newly identified lines exhibited high level of similarity among themselves as revealed by RAPD and STS markers (>92% and 80% respectively). Along with the enrichment in genetic resources of Stylosanthes, these newly identified and characterized accessions of S. seabrana can be better exploited in breeding programs targeted to quality.     

The strategy and potential utilization of temperate germplasm for tropical germplasm improvement: a case study of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

The organization of maize (Zea mays L.) germplasm into genetically divergent heterotic groups is the foundation of a successful hybrid maize breeding program. In this study, 94 CIMMYT maize lines (CMLs) and 54 United States germplasm enhancement of maize (GEM) lines were assembled and characterized using 1,266 single nucleotide polymorphisms (SNPs) with high quality. Based on principal component analysis (PCA), the GEM lines and CMLs were clearly separated. In the GEM lines, there were two groups classified by PCA corresponding to the heterotic groups “stiff stalk” and “non-stiff stalk”. CMLs did not form obvious subgroups by PCA. The allelic frequency of each SNP differed in GEM lines and CMLs. In total, 3.6% alleles (46/1,266) of CMLs are absent in GEM lines and 4.4% alleles (56/1,266) of GEM lines are absent in CMLs. The performance of F1 plants (n = 654) produced by crossing between different groups based on pedigree information was evaluated at the breeding nurseries of two CIMMYT stations. Genomic estimated phenotypic values of plant height and days to anthesis for a testing set of 45 F1 crosses were predicted based on the training data of 600 F1 crosses using a best linear unbiased prediction method. The prediction accuracy benefitted from the adoption of the markers associated with quantitative trait loci for both traits; however, it does not necessarily increase with an increase in marker density. It is suggested that genomic selection combined with association analysis could improve prediction efficiency and reduce cost. For hybrid maize breeding in the tropics, incorporating GEM lines which have unique alleles and clear heterotic patterns into tropically adapted lines could be beneficial for enhancing heterosis in grain yields.     

Assessment of testcross performance and genetic diversity of yellow endosperm maize lines derived from adapted × exotic backcrosses

Introduction of exotic maize (Zea mays L.) into adapted tropical germplasm may enhance genetic variability and lead to greater progress from selection. The first objective of this study was to determine if yellow endosperm lines derived from adapted × exotic backcrosses contain exotic alleles that are superior to the recurrent adapted parental line for yield and other agronomic traits in tropical environments. Thirteen exotic yellow maize inbred lines were crossed to an adapted orange line (KUSR) and the F₁s were backcrossed to KUSR to generate the first backcrosses. Fifty BC₁F₄ lines derived from these backcrosses and the recurrent parent were crossed to a common inbred tester (L4001) to form testcrosses, which were evaluated at eight environments in Nigeria. Testcrosses of the BC-derived lines differed significantly for grain yield and other agronomic traits. Only two testcrosses yielded significantly less than L4001 × KUSR, with the best 15 testcrosses producing between 289 and 1,056 kg/ha more grain yield than L4001 × KUSR. The best testcrosses were similar to or better than L4001 × KUSR for other agronomic traits. The second objective of this study was to assess the extent of genetic diversity present among the BC-derived lines. We genotyped 46 BC-derived lines including KUSR and L4001 with 10 AFLP primer pairs and found 491 polymorphic fragments. The average allelic diversity of the lines was 0.30 ± 0.01. The genetic distance of each BC-derived line from KUSR ranged between 0.49 and 0.91. The average genetic distance for all pairs of the BC-derived lines was 0.68 ± 0.004, varying from 0.34 to 0.92. The increased grain yield and genetic diversity observed in these studies provide evidence that exotic germplasm can contribute new alleles to expand the genetic base of tropical maize and develop high-yielding hybrids.     

High‐throughput genotyping for species identification and diversity assessment in germplasm collections

Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high‐throughput genotyping tools can provide a fast, efficient and cost‐effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A‐ and C‐genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high‐throughput molecular genotyping will offer an efficient and cost‐effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.     

Patterns of molecular variation in a species-wide germplasm set of <Emphasis Type="Italic">Brassica napus</Emphasis>

Rapeseed (Brassica napus L.) is the leading European oilseed crop serving as source for edible oil and renewable energy. The objectives of our study were to (i) examine the population structure of a large and diverse set of B. napus inbred lines, (ii) investigate patterns of genetic diversity within and among different germplasm types, (iii) compare the two genomes of B. napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B. napus inbred lines genotyped with 89 genome-specific SSR primer combinations. Both a principal coordinate analysis and software STRUCTURE revealed that winter types, spring types, and swedes were assigned to three major clusters. The genetic diversity of winter oilseed rape was lower than the diversity found in other germplasm types. Within winter oilseed rape types, a decay of genetic diversity with more recent release dates and reduced levels of erucic acid and glucosinolates was observed. The percentage of linked SSR loci pairs in significant (r ² > Q _{95 unlinked loci pairs}) LD was 6.29% for the entire germplasm set. Furthermore, LD decayed rapidly with distance, which will allow a relatively high mapping resolution in genome-wide association studies using our germplasm set, but, on the other hand, will require a high number of markers.     

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance

Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non‐additive genetic variation, we present an approach using genome‐wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein–Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome‐wide markers were tested for associations between heterozygosity and bTB status using marker‐based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy‐Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome‐wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy‐number‐variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large‐scale data.     

Genetic analysis of vertical root pulling resistance (VRPR) in maize using two genetic populations

Root traits are important in improving nutrient and water use efficiency. Vertical root pulling resistance (VRPR) has been shown to be closely related to root system characteristics in maize (Zea mays L.). In the present study, two genetic populations derived from the same parents, one containing 218 recombinant inbred lines (RILs) and the other containing 187 advanced backcross BC₄F₃ lines, were genotyped using 184 SSR markers and evaluated for VRPR, grain yield (GY), stover yield (SY), and nitrogen uptake (N_up) under field conditions over 2 years. Our aims were (1) to locate QTLs associated with VRPR, SY, GY, and N_up, (2) to determine whether QTL detection is consistent between the BC₄F₃ and RIL populations, and (3) to identify backcross lines harboring favorable VRPR QTLs for use in future breeding programs. Using composite interval mapping (CIM), 12 and 17 QTLs were detected in BC₄F₃ and RIL populations, respectively. An important QTL region in bin 6.02 within the interval umc1006-umc1257 was found to control VRPR, SY, and N_up in both populations. These favorable alleles were contributed by the large-rooted parent Ye478. A significant positive correlation was detected between VRPR, SY, and N_up, but not between VRPR and GY. Backcross lines harboring VRPR QTLs could be useful germplasm for developing near isogenic lines (NILs) and for map-based cloning of genes controlling root growth.     

Relationship of restriction fragment length polymorphisms to single-cross hybrid performance of maize

Summary Isozymes and restriction fragment length polymorphisms (RFLPs) have been proposed for use in varietal identification and selection for agronomic traits. Although the use of isozymes for these purposes has been well documented, evaluation of the efficacy of RFLP technology as applied to crop improvement is far from complete. This investigation was conducted to study the relationship between RFLP-derived genotypes and heterotic patterns of a group of maize (Zea mays L.) inbred lines. A total of 22 inbreds was crossed to four testers (B73, B76, Mo17, and Va26) in combinations that minimized crossing within heterotic groups. Forty-seven single-cross progeny were subsequently evaluated for several agronomic traits (including grain yield and moisture, ear height, and root lodging) over 2–4 consecutive years at two to four Iowa locations in a randomized complete-block design. The inbred lines were subjected to RFLP analysis, which involved 47 genomic clones and the restriction enzymes EcoRI and HindIII. Hybrid RFLP patterns were predicted from their inbred parents. Modified Roger's distances were computed to estimate genetic distance among the inbred lines. Principal component analysis facilitated ascertainment of relative dispersion of the inbreds based on the frequency of variants at specific RFLP loci. Evident associations of variants with genes affecting agronomic traits were identified by principal component regression analysis, in which adjusted hybrid means were regressed on the matrix of hybrid variants frequencies. The hybrid means were adjusted by removing environmental effects, using residuals as dependent variables in the regression analysis. Results from this study suggest that RFLP analysis may be of value in allocating maize inbreds to heterotic groups, but no relationship between RFLP-based genetic distance and hybrid performance was apparent. Principal component regression identified variants potentially linked to genes that control specific agronomic traits.Joint contribution: USDA-ARS and Journal Paper No. J-13590 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011, USA. Projects No. 2818 and 2778     

The role of environmental, root, and microbial biomass characteristics in soil respiration in temperate secondary forests of Northeast China

For secondary forests, the major forest resources in China (accounting for more than 50% of the national total), soil respiration (R _S) and the relationship between R _S and various biotic/abiotic factors are poorly understood. The objectives of the present study were to examine seasonal variations in soil respiration during the growing season, and to explore the factors affecting the variation in soil respiration rates for three forest types (Mongolian oak, Manchurian walnut and mixed forests) of temperate secondary forest in Northeast China. The results showed that (1) the maximum total R _S rate occurred in July, following a bell-shaped curve with season, (2) for all forest types, the total R _S was significantly influenced by soil temperature (P < 0.01), and did not significantly correlate with soil moisture, (3) compared with fine root biomass, coarse root biomass was more closely related with the root respiration in mixed forest (R ² = 0.711, P = 0.017) and in Manchurian walnut forest (R ² = 0.768, P = 0.010), and (4) microbial biomass carbon (MBC) and nitrogen were significantly correlated with heterotrophic R _S in Mongolian oak forest (R ² = 0.664, P = 0.026; R ² = 0.784, P = 0.008, respectively) and in mixed forest (R ² = 0.918, P = 0.001; R ² = 0.967, P = 0.001, respectively). We can conclude that in temperate secondary forests: (1) the R _S rate and the relationships between R _S and abiotic/biotic factors change greatly with forest types, and (2) R _S is strongly influenced by soil temperature, MBC, microbial biomass nitrogen and coarse root biomass in temperate secondary forests.     

Evaluation of reduced subsets of single nucleotide polymorphisms for the prediction of age at puberty in sows

Genomic information could be used efficiently to improve traits that are expensive to measure, sex limited or expressed late in life. This study analyzed the phenotypic variation explained by major SNPs and windows for age at puberty in gilts, an indicator of reproductive longevity. A genome‐wide association study using 56 424 SNPs explained 25.2% of the phenotypic variation in age at puberty in a training set (n = 820). All SNPs from the top 10% of 1‐Mb windows explained 33.5% of the phenotypic variance compared to 47.1% explained by the most informative markers (n = 261). In an evaluation population, consisting of subsequent batches (n = 412), the predictive ability of all SNPs from the major 1‐Mb windows was higher compared to the variance captured by the most informative SNP from each of these windows. The phenotypic variance explained in the evaluation population varied from 12.3% to 36.8% when all SNPs from major windows were used compared to 6.5–23.7% explained by most informative SNPs. The correlation between phenotype and genomic prediction values based on SNP effects estimated in the training population was marginal compared to their effects retrained in the evaluation population for all (0.46–0.81) or most informative SNPs (0.30–0.65) from major windows. An increase in genetic gain of 20.5% could be obtained if genomic selection included both sexes compared to females alone. The pleiotropic role of major genes such as AVPR1A could be exploited in selection of both age at puberty and reproductive longevity.     

Genome‐wide association analyses reveal the genetic basis of combining ability in rice

Combining ability is a measure for selecting elite parents and predicting hybrid performance in plant breeding. However, the genetic basis of combining ability remains unclear and a global view of combining ability from diverse mating designs is lacking. We developed a North Carolina II (NCII) population of 96 Oryza sativa and four male sterile lines to identify parents of greatest value for hybrid rice production. Statistical analyses indicated that general combining ability (GCA) and specific combining ability (SCA) contributed variously to different agronomic traits. In a genome‐wide association study (GWAS) of agronomic traits, GCA and SCA, we identified 34 significant associations (P < 2.39 × 10^?7). The superior alleles of GCA loci (Ghd8, GS3 and qSSR4) accumulated in parental lines with high GCA and explained 30.03% of GCA variance in grain yield, indicating that molecular breeding of high GCA parental lines is feasible. The distinct distributions of these QTLs contributed to the differentiation of parental GCA in subpopulations. GWAS of SCA identified 12 more loci that showed dominance on corresponding agronomic traits. We conclude that the accumulation of superior GCA and SCA alleles is an important contributor to heterosis and QTLs that greatly contributed to combining ability in our study would accelerate the identification of elite inbred lines and breeding of super hybrids.     

Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple crosses among Gossypium tetraploid species

Genetic improvement in yield and fiber quality is needed for worldwide cotton production. Identification of molecular markers associated with fiber-related traits can facilitate selection for these traits in breeding. This study was designed to identify associations between SSR markers and fiber traits using an exotic germplasm population, species polycross (SP), derived from multiple crosses among Gossypium tetraploid species. The SP population underwent 11 generations of mixed random mating and selfing followed by 12 generations of selfing. A total of 260 lines were evaluated for fiber-related traits under three environments in 2005 and 2006. Large genotypic variance components in traits were identified relative to components of genotype × environment. Eighty-six primer pairs amplified a total of 314 polymorphic fragments among 260 lines. A total of 202 fragments with above 6% allele frequency were analyzed for associations. Fifty-nine markers were found to have a significant (P < 0.05, 0.01, or 0.001) association with six fiber traits. There were six groups identified within the population using structure analysis. Allele frequency divergence among six groups ranged from 0.11 to 0.27. Of the 59 marker–trait associations, 39 remained significant after correction for population structure and kinship using a mixed linear model. The effect of population sub-structure on associations was most significant in boll weight among the traits analyzed. The sub-structure among the SP lines may be caused by natural selection, the breeding method applied during development of inbred lines, and unknown factors. The identified marker–trait associations can be useful in breeding and help determine genetic mechanisms underlying interrelationships among fiber traits. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

基于农艺性状的山西普通菜豆初级核心种质构建

利用663份山西省普通菜豆资源基于14个农艺性状,采用比较不同分组原则、取样比例和总体取样量不同组合的取样方法,确定了"地理来源+平方根比例+20%总体取样量"为山西省初级核心种质构建的方法。同时,在此基础上对663份资源中一些具有极端性状的资源进行选择,最终确定152份普通菜豆可作为山西省普通菜豆初级核心种质。通过总体与初级核心种质资源多样性分析,数量性状均值比较,数量性状极值、变幅和标准差比较,性状多样性的差异性分析和各性状总体分布的χ2检验,最终得出:152份普通菜豆资源能够代表山西省普通菜豆资源的总体,可作为山西省普通菜豆评价和创新利用的优先样品集。     

Phenotypic and molecular characterization of selected tomato recombinant inbred lines derived from the cross <Emphasis Type="Italic">Solanum lycopersicum</Emphasis> × <Emphasis Type="Italic">S. pimpinellifolium</Emphasis>

An important trait defining fresh tomato marketability is fruit shelf life. Exotic germplasm of Solanum pimpinellifolium is able to prolong shelf life. Sixteen recombinant inbred lines with differing values of shelf life and fruit weight were derived by antagonistic-divergent selection from an interspecific cross involving Solanum pimpinellifolium. The objective of this study was to evaluate these recombinant inbred lines for many fruit quality traits such as diameter, height, size, acidity, colour, firmness, shelf life and weight, and to characterize them by amplified fragment length polymorphism markers. For most traits, a wide range of genetic variability was found and a wide range of molecular variation was also detected. Both sets of data allowed the identification of recombinant inbred lines by means of cluster analysis and principal component analysis. Genetic association among some amplified fragment length polymorphism markers and fruit quality traits, suggested by the principal component analysis, could be identified by single point analysis. Potential molecular markers underlying agronomical traits were detected in these recombinant inbred lines.     

Leaf traits of two Mediterranean perennial tussock grass species in relation to soil nitrogen and phosphorus availability

Studying relationships of plant traits to ecosystem properties is an emerging approach aiming to understand plant's potential effect on ecosystem functioning. In the current study, we explored links between morphological and nutritional leaf traits of two Mediterranean perennial grass species Stipa tenacissima and Lygeum spartum, widely used to prevent desertification process by stabilizing sand dunes. We evaluated also relationships in terms of nitrogen (N) and phosphorus (P) availability between leaves of the investigated species and the corresponding soil. Our results showed that leaf P was very low in comparison with leaf N for the two investigated species. In fact, chlorophyll content, photosynthesis capacity and water conservation during photosynthesis are mainly linked to leaf nitrogen content. Our findings support previous studies showing that at the species levels, morphological and nutritional leaf traits were not related. On the other hand, significant relationships were obtained between soil N and leaf N for S. tenacissima (P = 0.011) and L. spartum (P = 0.033). However, leaf P was not significantly related to soil P availability for both species. We suggest that any decrease in soil N with the predicted increasing aridity may result in reduction in leaf N and thus in worst dysfunction of some biological processes levels.     

Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot

According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean π _sil = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F _ST = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r ²  = 0.635) within the 700–1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.     

Association of interleukin‐27 gene polymorphisms with susceptibility to HIV infection and disease progression

Interleukin‐27 (IL‐27) gene polymorphisms are linked to infectious disease susceptibility and IL‐27 plasma level is associated with HIV infection. Therefore, we aimed to investigate the association between IL‐27 polymorphisms and susceptibility to HIV infection and disease progression. A total of 300 patients with HIV infection (48 long‐term nonprogressors and 252 typical progressors) and 300 healthy controls were genotyped for three IL‐27 polymorphisms, rs17855750, rs181206, rs40837 which were performed by using multiple single nucleotide primer extension technique. Significant association was found between IL‐27 rs40837 polymorphisms with susceptibility to HIV infection (AG vs AA: adjusted OR = 1.60, 95% CI, 1.11‐2.30, P = 0.012; AG+GG vs AA: adjusted OR = 1.44, 95% CI, 1.02‐2.03, P = 0.038) and disease progression (LTNP: AG vs AA: adjusted OR = 2.33, 95% CI, 1.13‐4.80, P = 0.021; TP: AG vs AA: adjusted OR = 1.50, 95% CI, 1.04‐2.24, P = 0.030). Serum IL‐27 levels were significantly lower in cases compared to controls (P < 0.001). There were lower serum IL‐27 levels in TPs than in LTNPs (P < 0.001). We further found that LTNPs with rs40837 AG or GG genotype had lower serum IL‐27 levels than with AA genotype (P < 0.05). The CD4⁺T counts in cases were significantly lower than controls (P < 0.001). In contrast, individuals with rs40837 AG genotype had lower CD4⁺T counts than with AA genotype in cases (P < 0.05). In addition, CD4⁺T counts in TPs were significantly lower than LTNPs (P < 0.001). IL‐27 rs40837 polymorphism might influence the susceptibility to HIV infection and disease progression probably by regulating the level of serum IL‐27 or the quantity of CD4⁺T.