Variability in reproductive traits in Jatropha curcas L. accessions during early developmental stages under warm subtropical conditions

Variability in floral, fruit, and seed characteristics, and oil content of 15 accession of Jatropha curcas during early development were assessed during two flowering periods in south Florida subtropical climate. The two flowering periods had leaf flushing in March. Field evaluation using 18 quantitative traits showed significant variation among accessions. The number of female flowers and female : male flower ratio ranged from 1 to 15 and 1 : 8.8 to 1 : 67.8, respectively. Fruit set by natural pollination was 89 and 66% during the first (1st) and second (2nd) flowering periods, respectively. A higher number of female‐type inflorescences were observed during summer. There were significant differences in seed traits, except for number of seeds per fruit. Accession TREC 31 had the highest individual seed dry weight and 100‐seed weight (0.83 g and 79.7 g, respectively). The oil content varied from 19.30% to 35.62%. Seed dry weight had positive correlation with seed fresh weight, seed length, seed thickness, seed width, and 100‐seed weight, but negative correlation with oil content. Based on the cluster analysis using 15 morphological traits, jatropha accessions were grouped into five main clusters and accessions from different geographic regions grouped together in a cluster. Principal component analyses (PCA) revealed morphological variation. The first three components explained 73.5% of the total variation and seed dry weight, 100‐seed weight, total flowers per inflorescence, male flowers per inflorescence and fruit set can be used to distinguish accessions. The PCA also indicated that flowering traits were more influenced by seed origin while seed traits were affected by flowering spans. Although evaluations were performed in plants during the juvenile phase, accessions TREC 31 and TREC 55 had superior averages for almost all characters evaluated. These results provide a preliminary assessment of the high variability in jatropha accessions evaluated and their potential for use in breeding and genetic improvement programs.     

Natural variation in GmGBP1 promoter affects photoperiod control of flowering time and maturity in soybean

The present study screened for polymorphisms in coding and non‐coding regions of the GmGBP1 gene in 278 soybean accessions with variable maturity and growth habit characteristics under natural field conditions in three different latitudes in China. The results showed that the promoter region was highly diversified compared with the coding sequence of GmGBP1. Five polymorphisms and four haplotypes were closely related to soybean flowering time and maturity through association and linkage disequilibrium analyses. Varieties with the polymorphisms SNP_‐796G, SNP_‐770G, SNP_‐307T, InDel_‐242normal, SNP_353A, or haplotypes Hap‐3 and Hap‐4 showed earlier flowering time and maturity in different environments. The shorter growth period might be largely due to higher GmGBP1 expression levels in soybean that were caused by the TCT‐motif with SNP_‐796G in the promoter. In contrast, the lower expression level of GmGBP1 in soybean caused by RNAi interference of GmGBP1 resulted in a longer growth period under different day lengths. Furthermore, the gene interference of GmGBP1 also caused a reduction in photoperiod response sensitivity (PRS) before flowering in soybean. RNA‐seq analysis on GmGBP1 underexpression in soybean showed that 94 and 30 predicted genes were significantly upregulated and downregulated, respectively. Of these, the diurnal photoperiod‐specific expression pattern of three significant flowering time genes GmFT2a, GmFT5a, and GmFULc also showed constantly lower mRNA levels in GmGBP1‐i soybean than in wild type, especially under short day conditions. Together, the results showed that GmGBP1 functioned as a positive regulator upstream of GmFT2a and GmFT5a to activate the expression of GmFULc to promote flowering on short days.     

A histone methyltransferase inhibits seed germination by increasing PIF1 mRNA expression in imbibed seeds

Phytochrome‐interacting factor 1 (PIF1) inhibits light‐dependent seed germination. The specific function of PIF1 in seed germination is partly due to its high level of expression in imbibed seeds, but the associated regulatory factors have not been identified. Here we show that mutation of the early flowering in short days (EFS) gene, encoding an H3K4 and H3K36 methyltransferase, decreases the level of H3K36me2 and H3K36me3 but not H3K4me3 at the PIF1 locus, reduces the targeting of RNA polymerase II to the PIF1 locus, and reduces mRNA expression of PIF1 in imbibed seeds. Consistently, the efs mutant geminated even under the phyB_off condition, and had an expression profile of PIF1 target genes similar to that of the pif1 mutant. Introduction of an EFS transgene into the efs mutant restored the level of H3K36me2 and H3K36me3 at the PIF1 locus, the high‐level expression of PIF1 mRNA, the expression pattern of PIF1 target genes, and the light‐dependent germination of these seeds. Introduction of a PIF1 transgene into the efs mutant also restored the expression pattern of PIF1 target genes and light‐dependent germination in imbibed seeds, but did not restore the flowering phenotype. Taken together, our results indicate that EFS is necessary for high‐level expression of PIF1 mRNA in imbibed seeds.     

Spatio‐temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana

The evolutionary response of organisms to global climate change is expected to be strongly conditioned by preexisting standing genetic variation. In addition, natural selection imposed by global climate change on fitness‐related traits can be heterogeneous over time. We estimated selection of life‐history traits of an entire genetic lineage of the plant Arabidopsis thaliana occurring in north‐western Iberian Peninsula that were transplanted over multiple years into two environmentally contrasting field sites in southern Spain, as southern environments are expected to move progressively northwards with climate change in the Iberian Peninsula. The results indicated that natural selection on flowering time prevailed over that on recruitment. Selection favored early flowering in six of eight experiments and late flowering in the other two. Such heterogeneity of selection for flowering time might be a powerful mechanism for maintaining genetic diversity in the long run. We also found that north‐western A. thaliana accessions from warmer environments exhibited higher fitness and higher phenotypic plasticity for flowering time in southern experimental facilities. Overall, our transplant experiments suggested that north‐western Iberian A. thaliana has the means to cope with increasingly warmer environments in the region as predicted by trends in global climate change models.     

Genome‐wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola

Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola‐meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome‐wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome‐wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes.     

Gibberellic acid signaling is required for ambient temperature‐mediated induction of flowering in Arabidopsis thaliana

Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature‐dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15°C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.     

Quantitative trait loci for flowering time and inflorescence architecture in rose

The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F ₁ diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose.     

Heritable variation in the inflorescence replacement program of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Owing to their sessile habits and trophic position within global ecosystems, higher plants display a sundry assortment of adaptations to the threat of predation. Unlike animals, nearly all higher plants can replace reproductive structures lost to predators by activating reserved growing points called axillary meristems. As the first step in a program aimed at defining the genetic architecture of the inflorescence replacement program (IRP) of Arabidopsis thaliana, we describe the results of a quantitative germplasm survey of developmental responses to loss of the primary reproductive axis. Eighty-five diverse accessions were grown in a replicated common garden and assessed for six life history traits and four IRP traits, including the number and lengths of axillary inflorescences present on the day that the first among them re-flowered after basal clipping of the primary inflorescence. Significant natural variation and high heritabilities were observed for all measured characters. Pairwise correlations among the 10 focal traits revealed a multi-dimensional phenotypic space sculpted by ontogenic and plastic allometries as well as apparent constraints and outliers of genetic interest. Cluster analysis of the IRP traits sorted the 85 accessions into 5 associations, a topology that establishes the boundaries within which the evolving Arabidopsis genome extends and restricts the species’ IRP repertoire to that observable worldwide.     

Natural variation in Early flowering1 contributes to early flowering in japonica rice under long days

Natural variation in heading‐date genes enables rice, a short‐day (SD) plant, to flower early under long‐day (LD) conditions at high latitudes. Through analysis of heading‐date quantitative trait loci (QTL) with F₇ recombinant inbred lines from the cross of early heading ‘H143’ and late heading ‘Milyang23 (M23)’, we found a minor‐effect Early Heading3 (EH3) QTL in the Hd16 region on chromosome 3. We found that Early flowering1 (EL1), encoding casein kinase I (CKI), is likely to be responsible for the EH3/Hd16 QTL, because a missense mutation occurred in the highly conserved serine/threonine kinase domain of EL1 in H143. A different missense mutation was found in the EL1 kinase domain in Koshihikari. In vitro kinase assays revealed that EL1/CKI in H143 and Koshihikari are non‐functional. In F_7:9 heterogeneous inbred family‐near isogenic lines (HNILs), HNIL(H143) flowered 13 days earlier than HNIL(M23) in LD, but not in SD, in which EL1 mainly acts as a LD‐dependent flowering repressor, down‐regulating Ehd1 expression. In the world rice collection, two types of non‐functional EL1 variants were found in japonica rice generally cultivated at high latitudes. These results indicate that natural variation in EL1 contributes to early heading for rice adaptation to LD in temperate and cooler regions.     

Natural variation involving deletion alleles of FRIGIDA modulate temperature‐sensitive flowering responses in Arabidopsis thaliana

Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu‐0 accession in long days. Genetic mapping in the Col‐0 × Tsu‐0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu‐0 FRI allele, which is the same as FRI‐Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI‐Ler allele confers temperature‐sensitive late flowering confirming a role for FRI in photoperiod‐dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis‐regulatory variation at FT contributes to the observed hypersensitivity of Tsu‐0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod‐dependent thermal responses of A. thaliana.     

Floral initiation in Rudbeckia hirta (Asteraceae) under limited inductive photoperiodic treatments

Two experiments were conducted to examine the response of Rudbeckia hirta to limited inductive photoperiodic treatments. The first examined the effects on plants grown to an thesis of the second axillary inflorescence, and the second examined the early histological events within the meristem. Plants of Rudbeckia hirta were grown to maturity under short days (SD). At maturity, half the plants were placed in long days (LD). In the first experiment, the plants remained under LD for 0, 8, 16, 24, or 32 days before being returned to SD with an additional group remaining under LD as a control. In the second experiment, the plants remained under LD for 0, 4, 8, 12, 16, 20, 24, or 28 days before being returned to SD. Meristems were sampled 0, 4, 8, or 12 days after return to SD and histologically examined. Four groups of plants receiving 32, 36, 40, or 44 LD were used as a continuous LD control. When grown to anthesis, plant height and branch number increased as the number of inductive cycles increased. Plants receiving 24 or more LD reached anthesis earlier than plants receiving fewer LD. Histological examination of plants receiving only 4 LD showed they never progressed beyond early floral initiation. After 12 LD, the meristems continued to develop even when returned to SD, indicating that enough of the floral stimulus had reached the meristem to initiate flowering. Once involucral bract primordia initiated, floral development continued whether in LD or SD conditions.     

Differential genetic variation in adaptive strategies to a common environmental signal in Arabidopsis accessions: phytochrome-mediated shade avoidance

Shade avoidance is a syndrome of plastic responses to light signals encountered in crowded plant communities and is a crucial component of competitive strategy in higher plants. The responses are mediated via signal perception by specific members of the phytochrome family of photoreceptors, which detect the relative proportions of red (R) and far‐red (FR) radiation within dense communities. We analysed two aspects of shade avoidance, the acceleration of flowering and the enhancement of elongation growth, displayed by more than 100 accessions of Arabidopsis thaliana (Heyn.) in response to FR‐proximity signals. Both traits showed wide variation between accessions, which was unrelated to the latitude of the location of original collection. Flowering acceleration is a major feature of shade avoidance in rosette plants such as Arabidopsis, and most accessions showed dramatic responses, but several were identified as being recalcitrant to the proximity signal. These accessions are likely to be informative in the analysis of quantitative variation in shade avoidance. Hypocotyl elongation, treated here as an indicator of elongation growth responses, also varied widely amongst accessions. The variations in flowering acceleration and elongation were not correlated, indicating that microevolution in the downstream pathways from signal perception has occurred separately.     

Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China

The genetic diversity, population structure, and linkage disequilibrium (LD) of peaches are greatly important in genome-wide association mapping. In the current study, 104 peach landrace accessions from six Chinese geographical regions were evaluated for fruit and phenological period. The accessions were genotyped with 53 genome-wide simple sequence repeat (SSR) markers. All SSR markers were highly polymorphic across the accessions, and a total of 340 alleles were detected, including 59 private alleles. Of the six regions studied, the northern part of China as well as the middle and lower reaches of the Changjiang River were found to be the most highly diverse genetically. Based on population structure analysis, the peaches were divided into five groups, which well agreed with the geographical distribution. Of the SSR pairs in these accessions, 18.07% (P?<?0.05) were in LD. The mean r ² value for all intrachromosomal loci pairs was 0.0149, and LD decayed at 6.01?cM. The general linear model was used to calculate the genome-wide marker-trait associations of 10 complex traits. The traits include flesh color around the stone, red pigment in the flesh, flesh texture, flesh adhesion, flesh firmness, fruit weight, chilling requirement, flowering time, ripening time, and fruit development period. These traits were estimated by analyzing the 104 landraces. Many of the associated markers were located in regions where quantitative trait loci (QTLs) were previously identified. Peach association mapping is an effective approach for identifying QTLs and may be an alternative to QTL mapping based on crosses between different lines.     

Molecular,genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17‐Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F‐box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col‐FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South‐Eastern Europe approximately 5000 years ago and the FRI‐Col allele to North‐West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The ‘American haplotype’ was identified from several European localities, potentially due to return migration.     

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.     

Adaptation of Maize to Temperate Climates: Mid-Density Genome-Wide Association Genetics and Diversity Patterns Reveal Key Genomic Regions,with a Major Contribution of the Vgt2 (ZCN8) Locus

The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the ZCN8 gene, which is the closest maize homologue to Arabidopsis major flowering time (FT) gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of Vgt2 QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD) estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide range of environments.     

Relation among plant growth,carbohydrates and flowering time in the Arabidopsis Landsberg erecta × Kondara recombinant inbred line population

Arabidopsis thaliana natural variation was used to study plant performance viewed as the accumulation of photo‐assimilates, their allocation and storage, in relation to other growth‐related features and flowering‐related traits. Quantitative trait locus (QTL) analysis using recombinant inbred lines derived from the cross between Landsberg erecta (originating from Poland) and Kondara (originating from Tajikistan) grown on hydroponics, revealed QTLs for the different aspects of plant growth‐related traits, sugar and starch contents and flowering‐related traits. Co‐locations of QTLs for these different aspects were detected at different regions, mainly at the ER locus; the top of chromosomes 3, 4 and 5; and the bottom of chromosome 5. Increased plant growth was associated with early flowering and leaf transitory starch, and correlated negatively with the levels of soluble sugar at early phases of development. From the significant correlations and the co‐locations of the QTLs for these aspects, we conclude that there is a complex relationship between plant growth‐related traits, carbohydrate content and flowering‐related traits.