Maize genetic diversity and association mapping using transposable element insertion polymorphisms

Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3′ end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation.     

Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines,as compared to the maize USDA genebank

Key message

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs.

Abstract

Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees–Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees–Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.

     

Cytologic findings in infiltrating micropapillary carcinoma and mucinous carcinomas with micropapillary pattern

OBJECTIVE: To examine the observation that some mucinous carcinomas have a micropapillary pattern and are mucinous variants of the highly angioinvasive infiltrating micropapillary carcinomas (IMPC). STUDY DESIGN: We evaluated cytologic findings of 13 IMPC and 55 mucinous carcinomas for comparative features. RESULTS: In mucinous carcinomas, 37 of 50 (74%) had a micropapillary pattern. This group included 27 cases with pure mucinous micropapillary morphology (MUMPC), 8 MUMPC associated with a ductal carcinoma of the IMPC type (MUIDC) and 2 cases of mixed mucinous carcinomas with an MUMPC and a solid variant ofpapillary carcinoma (SVPC) component. On cytology both IMPC and mucinous carcinomas with micropapillary pattern demonstrated the micropapillary pattern, that is, angulated clusters or abortive papillae and ball-like clusters. However, the IMPC smears revealed numerous singly scattered tumor cells and larger fragments with shrub-like branching and the MUMPC had psammoma bodies. The mixed MUMPC and SVPC showed the classic cytologic features of MUMPC admixed with abundant singly dispersed tumor cells in the background representing the SVPC component. CONCLUSION: Although IMPC and the MUMPC share the micropapillary pattern on histologic examination, mucin alters the appearances in aspirates. Recognition of this morphologic spectrum will help in understanding the behavior of these tumors.     

Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium

Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models.     

Dent and Flint maize diversity panels reveal important genetic potential for increasing biomass production

Key message

Genetic and phenotypic analysis of two complementary maize panels revealed an important variation for biomass yield. Flowering and biomass QTL were discovered by association mapping in both panels.

Abstract

The high whole plant biomass productivity of maize makes it a potential source of energy in animal feeding and biofuel production. The variability and the genetic determinism of traits related to biomass are poorly known. We analyzed two highly diverse panels of Dent and Flint lines representing complementary heterotic groups for Northern Europe. They were genotyped with the 50 k SNP-array and phenotyped as hybrids (crossed to a tester of the complementary pool) in a western European field trial network for traits related to flowering time, plant height, and biomass. The molecular information revealed to be a powerful tool for discovering different levels of structure and relatedness in both panels. This study revealed important variation and potential genetic progress for biomass production, even at constant precocity. Association mapping was run by combining genotypes and phenotypes in a mixed model with a random polygenic effect. This permitted the detection of significant associations, confirming height and flowering time quantitative trait loci (QTL) found in literature. Biomass yield QTL were detected in both panels but were unstable across the environments. Alternative kinship estimator only based on markers unlinked to the tested SNP increased the number of significant associations by around 40 % with a satisfying control of the false positive rate. This study gave insights into the variability and the genetic architectures of biomass-related traits in Flint and Dent lines and suggests important potential of these two pools for breeding high biomass yielding hybrid varieties.     

Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time

Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.     

Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst)

In order to analyze the large-scale structure of the genome of Norway spruce (Picea abies Karst.), a pseudo-testcross genetic linkage map was built using markers of six different types, belonging to the low (amplified fragment length polymorphisms, simple sequence repeats) or high (sequence-specific amplified polymorphisms, inter-retrotransposon amplified polymorphisms) copy-number fraction of the genome, and including expressed region-derived markers (expressed sequence tag polymorphisms). Twenty seven and 23 linkage groups of at least four markers were obtained for the female and the male parent maps, respectively. A subset of these linkage groups coalesced into 13 bi-parental linkage groups through markers shared between the two maps. This map was used to investigate the frequency of each marker type over chromosomes and the distribution of marker types relative to each other, using autocorrelation techniques. Our results show that, while the composition of chromosomes is homogeneous, low- and high-copy-number markers tend to occupy separate regions of the linkage groups, and that expressed sequences are preferentially associated with microsatellites and separated from retrotransposons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users.     

Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene

To investigate the genetic basis of maize adaptation to temperate climate, collections of 375 inbred lines and 275 landraces, representative of American and European diversity, were evaluated for flowering time under short- and long-day conditions. The inbred line collection was genotyped for 55 genomewide simple sequence repeat (SSR) markers. Comparison of inbred line population structure with that of landraces, as determined with 24 SSR loci, underlined strong effects of both historical and modern selection on population structure and a clear relationship with geographical origins. The late tropical groups and the early "Northern Flint" group from the northern United States and northern Europe exhibited different flowering times. Both collections were genotyped for a 6-bp insertion/deletion in the Dwarf8 (D8idp) gene, previously reported to be potentially involved in flowering time variation in a 102 American inbred panel. Among-group D8idp differentiation was much higher than that for any SSR marker, suggesting diversifying selection. Correcting for population structure, D8idp was associated with flowering time under long-day conditions, the deletion allele showing an average earlier flowering of 29 degree days for inbreds and 145 degree days for landraces. Additionally, the deletion allele occurred at a high frequency (>80%) in Northern Flint while being almost absent (<5%) in tropical materials. Altogether, these results indicate that Dwarf8 could be involved in maize climatic adaptation through diversifying selection for flowering time.     

FT genome A and D polymorphisms are associated with the variation of earliness components in hexaploid wheat

The transition from vegetative to floral meristems in higher plants is determined by the coincidence of internal and environmental signals. Contrary to the photoperiod pathway, convergent evolution of the cold-dependent pathway has implicated different genes between dicots and monocots. Whereas no association between natural variation in vernalization requirement and Flowering time locus T (FT) gene polymorphism has been described in Arabidopsis, recent studies in Triticeae suggest implication of orthologous copies of FT in the cold response. In our study, we show that nucleotide polymorphisms on A and D copies of the wheat FT gene were associated with variations for heading date in a collection of 239 lines representing diverse geographical origins and status (landraces, old or recent cultivars). Interestingly, polymorphisms in the non-coding intronic region were strongly associated to flowering variation observed on plants grown without vernalization. But differently from VRN1, no epistatic interaction between FT homeologous copies was revealed. In agreement with the results of association study, the A and D copies of FT were mapped in regions including major QTLs for earliness traits in hexaploid wheat. This work, by identifying additional homeoalleles involved in wheat vernalization pathway, will contribute to a better understanding of the control of flowering, hence providing tools for the breeding of varieties with enhanced adaptation to changing environments. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information

An association study conducted on 375 maize inbred lines indicates a strong relationship between Vgt1 polymorphisms and flowering time, extending former quantitative trait loci (QTL) mapping results. Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize altilatitudinal adaptation.