The data presented here provide a framework for choosing specific genotypes for correlations with large "omics" data sets being collected for Boechera to study population structure, gene flow, and evolution of specific traits. We hypothesize that low levels of apomeiosis represent an ancestral condition of Boechera, whereas high apomeiosis levels may have been induced by global gene regulatory changes associated with hybridization.

Apomixis (asexual seed production) is characterized by meiotically unreduced egg cell production (apomeiosis) followed by its parthenogenetic development into offspring that are genetic clones of the mother plant. Fertilization (i.e. pseudogamy) of the central cell is important for the production of a functional endosperm with a balanced 2:1 maternal:paternal genome ratio. Here, we present the APOLLO (for apomixis-linked locus) gene, an Aspartate Glutamate Aspartate Aspartate histidine exonuclease whose transcripts are down-regulated in sexual ovules entering meiosis while being up-regulated in apomeiotic ovules at the same stage of development in plants of the genus Boechera. APOLLO has both "apoalleles," which are characterized by a set of linked apomixis-specific polymorphisms, and "sexalleles." All apomictic Boechera spp. accessions proved to be heterozygous for the APOLLO gene (having at least one apoallele and one sexallele), while all sexual genotypes were homozygous for sexalleles. Apoalleles contained a 20-nucleotide polymorphism present in the 59 untranslated region that contains specific transcription factor-binding sites for ARABIDOPSIS THALIANA HOMEOBOX PROTEIN5, LIM1 (for LINEAGE ABNORMAL11, INSULIN1, MECHANOSENSORY PROTEIN3), SORLIP1AT (for SEQUENCES OVERREPRESENTED IN LIGHT-INDUCED PROMOTERS IN ARABIDOPSIS THALIANA1), SORLIP2AT, and POLYA SIGNAL1. In the same region, sexalleles contain transcription factorbinding sites for DNA BINDING WITH ONE FINGER2, DNA BINDING WITH ONE FINGER3, and PROLAMIN BOX-BINDING FACTOR. Our results suggest that the expression of a single deregulated allele could induce the cascade of events leading to asexual female gamete formation in an apomictic plant.

Asexual reproduction is expected to reduce the adaptive potential to novel or changing environmental conditions, restricting or altering the ecological niche of asexual lineages. Asexual lineages of plants and animals are typically polyploid, an attribute that may influence their genetic variation, plasticity, adaptive potential, and niche breadth. The genus Boechera (Brassicaceae) represents an ideal model to test the relative ecological and biogeographic impacts of reproductive mode and ploidy because it is composed of diploid sexual and both diploid and polyploid asexual (i.e., apomictic) lineages. Here, we demonstrate a strong association between a transcriptionally conserved allele and apomictic seed formation. We then use this allele as a proxy apomixis marker in 1,649 accessions to demonstrate that apomixis is likely to be a common feature across the Boechera phylogeny. Phylogeographic analyses of these data demonstrate (i) species-specific niche differentiation in sexuals, (ii ) extensive niche conservation between differing reproductive modes of the same species, (iii) ploidy-specific niche differentiation within and among species, and (iv) occasional niche drift between apomicts and their sexual ancestors. We conclude that ploidy is a substantially stronger and more common driver of niche divergence within and across Boechera species although variation in both traits may not necessarily lead to niche evolution on the species scale.Boechera | UPGRADE2 | APOLLO | geographic parthenogenesis | niche conservation

The genetic mechanisms causing seed development by gametophytic apomixis in plants are predominantly unknown. As apomixis is consistently associated with hybridity and polyploidy, these confounding factors may either A) be the underlying mechanism for the expression of apomixis, or B) obscure the genetic factors which cause apomixis. To distinguish between these hypotheses, we analyzed the population genetic patterns of diploid and triploid apomictic lineages and their sexual progenitors in the genus Boechera (Brassicaceae). We find that while triploid apomixis is associated with hybridization, the majority of diploid apomictic lineages are likely the product of intra-specific crosses. We then show that these diploid apomicts are more likely to sire triploid apomictic lineages than conspecific sexuals. Combined with flow cytometric seed screen phenotyping for male and female components of apomixis, our analyses demonstrate that hybridization is an indirect correlate of apomixis in Boechera. KeywordsBoechera; Apomixis; Apomeiosis; Hybridization; Polyploidy Sexual, outcrossing reproduction is the ancestral state of embryo development in flowering plants (Karron et al. 2012). This breeding system has generated much of the biodiversity on earth and provides species with the potential to adapt to changing conditions, thus improving the chance for long term survival. Despite these advantages, many groups of plants have independently evolved asexual methods to produce seed (van Dijk and Vijverberg 2005;Carman 1997). Among these mechanisms, gametophytic apomixis (hereon "apomixis") is one of the most common (Hörandl and Hojsgaard 2012 requires the coordination of several independent phenotypes including the formation of an unreduced embryo sac (female apomeiosis) and embryo development from an unfertilized and unreduced egg cell (parthenogenesis). Other traits, including the production of unreduced pollen (male apomeiosis) and the development of functional endosperm (e.g. pseudogamy) are typical of apomictic genotypes (Mogie 1992;Bicknell and Koltunow 2004). Considering that apomixis evolves from sexuality, the expression of any one of these traits alone would be deleterious. For example, female apomeiosis without parthenogenesis would lead to ploidy increases after each generation (although see Van Dijk & Vijverberg, 2005). The evolutionary mechanism causing the simultaneous establishment of these traits is the foremost debate in the apomixis literature.Many authors have suggested that the genome-wide affects of hybridization and polyploidy may induce apomixis (Carman 1997;Comai et al. 2003;Madlung et al. 2002;Sharbel et al. 2010; Wang et al. 2004) as evidenced by the nearly uniform pattern of hybridity and polyploidy in apomictic lineages (Pongratz et al. 1997;Bicknell and Koltunow 2004;Mogie 1986; Asker and Jerling 1992;Nelson-Jones et al. 2002). However, this correlation may be indirect: since apomictic lineages are expected to accumulate mutations through time (Hopf et al. 1988;Kondrashov 1985), hybridity ...

Multivariate analyses were carried out on fifty-nine germplasm accessions of cashew derived from both local and exotic populations established at the research plots of Cocoa Research Institute of Nigeria (CRIN), Ibadan, southwestern Nigeria, to assess the extent of variability and pattern of genetic diversity among these cashew populations. Data collected on 36 quantitative and 33 qualitative plant characters were subjected to taximetric tools of Euclidean distance of complete linkage (furthest neighbour) and principal component analysis (PCA). The multivariate analyses tentatively grouped the selections into four distinct morphogenetically diverse clusters. The groupings appear to be a function of origin, eco-geographical distribution, genetic and/or agronomic affinity of the selections. Brazilian populations distinctly clustered together in two major groups while local clones and Indian selections dominated the other two major clusters with each group having its unique fruiting and tree growth habits. The clustering pattern at sub-cluster levels clearly reflects affinity of each genetic population. The principal component analysis and the potency indices showed that fruit characters are the most discriminating parameters for delineating cashew at the varietal level.

The role of pollen-stigma interaction and pollen tube growth as a measure of genetic compatibility was studied in eleven clones of cashew under a tropical rainforest ecology in Southwestern Nigeria between 1999 and 2002. Diallel cross of the clones showed that 55.00% of the cross-pollinated crosses showed high pollen cross-compatibility (CC) indicating moderate genetic distance in the population. About 54.55% of the clones showed evidence of selfcompatibility, therefore confirming that cashew is self-fertile. Cytological examination however suggests possible postzygotic self-incompatibility in the crop as no evidence of tube growth inhibition was recorded in both cross-and self-pollinated styles. Correlation between maternal compatibility (pollen recipients) and fruit set shows that more attention need to be focused in this direction during selection. Based on the data from this study, the use of combinations of floral quality characteristics like high pollen fertility, prolific flowering, and high flower sex ratio plus high cross-compatibility as reliable selection criteria for cashew yield improvement is therefore suggested.

Relationships between cashew nut yield and nine agronomic traits comprising seven reproductive (nut and floral) and two vegetative characters were studied in 59 selected cashew genotypes over three production seasons. Phenotypic correlation analysis showed that nuts per panicle (r = 0.844), number of nuts per tree (r = 0.988) and number of hermaphrodite flowers per panicle (r = 0.863) were positively correlated with nut yield and could be used as primary components for improving yield. Although correlation analysis showed insignificant association between nut weight and nut yield, path analysis revealed that the trait had significant positive direct effect (0.317) on nut yield. The subtle indirect effects of nut weight and leaf size on nut yield were more important than their direct effects and could be classified as secondary components. Both the direct and indirect effects of weight of the whole fruit and tree canopy on nut yield were negative and appeared detrimental.

The problem of declining tree yield has led to an investigation into the effectiveness of foliar application of exogenous hormones to improve flowering, fruit set, and fruit retention in cashew. Five exogenous hormones, one Gibberellic Acid (GA3) and four Auxins (IAA, IBA, NAA, and 2,4-D) at seven different rates of application (0 mg L -1 , 10 mg L -1 , 25 mg L -1 , 50 mg L -1 , 100 mg L -1 , 250 mg L -1 , and 500 mg L -1 ) were tested on six yield-related components of the two Brazilian cashew genotypes. This trial was a factorial split-split-plot design with each treatment replicated five times within a tree and three replications (three trees) per genotype. Responses varied significantly between exogenous hormones, concentrations and genotypes. The cashew plants used showed hormone-specific and optimum concentration response patterns. Of the five exogenous hormones tested, GA3 was most effective as its application at 50 -100 mg L -1 gave five-fold improvements in flowering (precocity and number of hermaphrodite flowers) and fruiting, and about 69% increase in fruit retention ability and 25% in nut size. Panicles treated with GA3 also produced relatively bigger nuts compared to the untreated. Days to flowering was found to be hormone sensitive, while production of hermaphrodite flowers, fruit set, and nut development tended to be concentration specific. The GA3 exhibited a broad concentration tolerance among the five exogenous hormones investigated. Our data showed that using GA3 at 50 mg L -1 will enhance flowering precocity, shorten flowering duration, increase production of hermaphrodite flowers and fruit set significantly, and resultant nuts develop optimally with high percentage retention. Thus, it suggests cashew yield could be increased by exogenous foliar application of GA3 at 50 -100 mg L -1 at preblooming stage.