B chromosome polymorphism in maize landraces: adaptive vs. demographic hypothesis of clinal variation

Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes

Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The North-Western Argentina (NWA) region constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the "Banco Activo de Germoplasma INTA Pergamino, Argentina" (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers. In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.

Intragenomic Conflict between Knob Heterochromatin and B Chromosomes Is the Key to Understand Genome Size Variation along Altitudinal Clines in Maize

In maize, we studied the causes of genome size variation and their correlates with cultivation altitude that suggests the existence of adaptive clines. To discuss the biological role of the genome size variation, we focused on Bolivian maize landraces growing along a broad altitudinal range. These were analyzed together with previously studied populations from altitudinal clines of Northwestern Argentina (NWA). Bolivian populations exhibited numerical polymorphism for B chromosomes (Bs) (from 1 to 5), with frequencies varying from 16.6 to 81.8 and being positively correlated with cultivation altitude. The 2C values of individuals 0B (A-DNA) ranged between 4.73 and 7.71 pg, with 58.33% of variation. The heterochromatic knobs, detected by DAPI staining, were more numerous and larger in individuals 0B than in those with higher doses of Bs. Bolivian and NWA landraces exhibited the same pattern of A-DNA downsizing and fewer and smaller knobs with increasing cultivation altitude, suggesting a mechanistic link among heterochromatin, genome size and phenology. The negative association between the two types of supernumerary DNA (knob heterochromatin and Bs), mainly responsible for the genome size variation, may be considered as an example of intragenomic conflict. It could be postulated that the optimal nucleotype is the result of such conflict, where genome adjustment may lead to an appropriate length of the vegetative cycle for maize landraces growing across altitudinal clines.

Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites-also known as simple sequence repeats (SSRs)-are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.

Cytological variations and long terminal repeat (LTR) retrotransposon diversities among diploids and B-chromosome aneuploids in Lilium amabile Palibin

BACKGROUND

B chromosomes are supernumerary chromosomes found in numerous plant species, including in the genus Lilium. Lilium amabile, an endemic Korean Lilium species, carries B chromosomes which are highly variable in terms of numbers and shape among the accessions collected throughout the Korea. Class 1 retrotransposons are highly abundant in the genome of Lilium species, but their biological functions are still obscure. Lilium species were known to hold high diversities derived from retrotransposons.

OBJECTIVE

In this study, genetic diversities among the L. amabile accessions were analyzed to better understand relationships between genetic variations and cytological diversities.

METHODS

Chromosomes were prepared from 95 L. amabile accessions for cytological identification. Genetic variations were analyzed by inter-retrotransposon amplified polymorphism (IRAP), and genetic differentiation was evaluated via Tajima's D neutrality and F_ST analyses. Population structure and phylogenetic analyses were also carried out.

RESULTS

The L. amabile accessions were classified into 11 cytotypes by the chromosome constitutions. Genetic diversity measured by IRAP analysis revealed high genetic diversity among the accessions. In the joint analysis of cytological variation with genetical variation, IRAP diversity was not related to the cytological diversities of diploid and aneuploids among L. amabile accessions, and genetic differentiation was not obvious. Moreover, the geographical distribution of L. amabile was not related to either IRAP diversity or cytological diversity.

CONCLUSION

The B chromosome-carrying aneuploids occurred randomly among diploids throughout Korea, and IRAP diversification predated L. amabile dispersion in Korea without genetic differentiation.

Evolution of Plant B Chromosome Enriched Sequences

B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences are not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes.

Exploring karyotype diversity of Argentinian Guaraní maize landraces: Relationship among South American maize

In Argentina there are two different centers of maize diversity, the Northeastern (NEA) and the Northwestern (NWA) regions of the country. In NEA, morphological studies identified 15 landraces cultivated by the Guaraní communities in Misiones Province. In the present study we analyzed the karyotype diversity of 20 populations of Guaraní maize landraces through classical and molecular cytogenetic analyses. Our results demonstrate significant intra and inter-populational variation in the percentage, number, size, chromosome position and frequencies of the heterochromatic blocks, which are called knobs. Knob sequence analysis (180-bp and TR-1) did not show significant differences among Guaraní populations. B chromosomes were not detected, and abnormal 10 (AB10) chromosomes were found with low frequency (0.1≥f ≤0.40) in six populations. Our results allowed karyotypic characterization of each analyzed population, defining for the first time the chromosomal constitution of maize germplasm from NEA. The multivariate analysis (PCoA and UPGMA) of karyotype parameters allowed the distinction between two populations groups: the Popcorn and the Floury maize populations. These results are in agreement with previously published microsatellite and morphological/phenological studies. Finally, we compared our karyotype results with those previously reported for NWA and Central Region of South America maize. Our data suggest that there are important differences between maize from NEA and NWA at the karyotype level, supporting the hypothesis that there are two pathways of input of South America maize. Our results also confirm the existence of two centers of diversification of Argentinian native maize, NWA and NEA. This work contributes new knowledge about maize diversity, which is relevant for future plans to improve commercial maize, and for conservation of agrobiodiversity.

Genome size variation in wild and cultivated maize along altitudinal gradients

It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.

Cytomolecular characterization of de novo formed rye B chromosome variants

BACKGROUND

B chromosomes (Bs) are dispensable elements which occur in many species including rye (Secale cereale). We determined the organization of B variants to obtain insights into the origin of B polymorphisms in rye.

RESULTS

The observed B variants were classified according to their morphology and in situ hybridization patterns with the B-specific repeats D1100 and CL11 into (I) long arm iso B, (II) D1100-deficient B and (III) small metacentric B variants. Long arm iso Bs are likely products of a meiotic centromere misdivision and subsequent duplication of the long arm, whereas small B variants are probably generated by chromosome breakage. Some deficient Bs experienced extensive amplification of CL11 repeats.

CONCLUSIONS

Both the pericentromere and the nondisjunction control region seem to be involved in the generation of rye B chromosome variants. However, due to the loss of the B-specific nondisjuction control region most of the variants generated are not capable to accumulate in a population.

Microsatellite variation in maize landraces from Northwestern Argentina: genetic diversity, population structure and racial affiliations

The highland region or Northwestern Argentina (NWA) is one of the southernmost areas of native maize cultivation and constitutes an expansion of the peruvian Andes sphere of influence. To examine the genetic diversity and racial affiliations of the landraces cultivated in this area, 18 microsatellite markers were used to characterize 147 individuals from 6 maize races representative of traditional materials. For the whole data set, a total of 184 alleles were found, with an average of 10.2 alleles per locus. The average gene diversity was 0.571. The observed patterns of genetic differentiation suggest that historical association is probably the main factor in shaping population structure for the landraces studied here. In agreement with morphological and cytogenetic data, Bayesian analysis of NWA landraces revealed the occurrence of three main gene pools. Assessment of racial affiliations using a combined dataset including previous data on American landraces showed a clear relationship between one of these gene pools and typical Andean races, whereas the remaining two gene pools exhibited a closer association to Caribbean accessions and native germplasm from the United States, respectively. These results highlight the importance of integrating regional genetic studies if a deeper understanding of maize diversification and dispersal is to be achieved.