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Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available.

A major QTL for grain dormancy, QPhs.ocs-3A.1, derived from the highly dormant wheat Zenkoujikomugi (Zen), has been identified in a study made under a controlled environment. Further investigations were needed to dissect the precise position and expression of QPhs.ocs-3A.1 under different field conditions because the ability to detect genetic loci for grain dormancy traits is compromised by environmental effects and genotype/environment interactions. Group 4 chromosomes have also been shown to be possible sites of QTLs for grain dormancy. The objectives of this study were (1) to locate additional molecular markers in the QPhs.ocs-3A.1 region, (2) to identify QTLs on the group 4 chromosomes and (3) to elucidate their combined effects. We examined the recombinant inbred lines (RILs) from a cross between Chinese Spring (CS) and Zen over a 3-year period in one location and 1 year in a different location. In an interval mapping study QPhs.ocs-3A.1 was mapped to within the 4.6 cM region flanked by Xbarc310 and Xbcd907 at the proximal end of the short arm of chromosome 3A. QPhs.ocs-3A.1 was confirmed to be the predominant dormancy QTL since it explained a large portion (11.6-44.8%) of the phenotypic variation, and was strongly displayed under dormancy-breaking conditions or at low germination temperatures. For QPhs.ocs-4A.1, identified on the long arm of chromosome 4A, and QPhs.ocs-4B.1, on the centromeric region of the long arm of Chr 4B, the LOD peak positions and the desirable allele were consistent between the trials, while the LOD scores and contribution to the phenotypic variation varied. Transgressive segregants were observed among the 125 RILs and most of them had a combination of the three alleles conferring a higher dormancy: the Zen alleles at QPhs.ocs-3A.1 and QPhs.ocs-4A.1 and the CS allele at QPhs.ocs-4B1. This demonstrated a combined effect of the desirable alleles on accelerating grain dormancy, with their total effect being superior to that of Zen.

Perfect timing of germination is required to encounter optimal conditions for plant survival and is the result of a complex interaction between molecular processes, seed characteristics, and environmental cues. To detangle these processes, we made use of natural genetic variation present in an Arabidopsis (Arabidopsis thaliana) Bayreuth X Shahdara recombinant inbred line population. For a detailed analysis of the germination response, we characterized rate, uniformity, and maximum germination and discuss the added value of such precise measurements. The effects of after-ripening, stratification, and controlled deterioration as well as the effects of salt, mannitol, heat, cold, and abscisic acid (ABA) with and without cold stratification were analyzed for these germination characteristics. Seed morphology (size and length) of both dry and imbibed seeds was quantified by using image analysis. For the overwhelming amount of data produced in this study, we developed new approaches to perform and visualize high-throughput quantitative trait locus (QTL) analysis. We show correlation of trait data, (shared) QTL positions, and epistatic interactions. The detection of similar loci for different stresses indicates that, often, the molecular processes regulating environmental responses converge into similar pathways. Seven major QTL hotspots were confirmed using a heterogeneous inbred family approach. QTLs colocating with previously reported QTLs and well-characterized mutants are discussed. A new connection between dormancy, ABA, and a cripple mucilage formation due to a naturally occurring mutation in the MUCILAGE-MODIFIED2 gene is proposed, and this is an interesting lead for further research on the regulatory role of ABA in mucilage production and its multiple effects on germination parameters.

Abstract Bidens pilosa L. is a heterocarpic weed species with two cypselae types that present morpho-physiological differences, being the peripheral type smaller and slower to germinate than the central one. We aimed to verify how the germination mechanism varied between types. We focused on two mechanisms: (1) pericarp constraints (physical and chemical) and (2) hormonal stimulation (Abcisic acid [ABA] and Gibberellin [GA]). Both cypselae types are physically constrained by the pericarp, for when it is excised both seed types increase their germination, but behavioral differences still remain. The pericarp of the peripheral type also has chemical inhibitors that effectively inhibited germination of the intact central cypsela. To test the hormonal effects, we focused on the ABA:GA control. Both cypselae responded to an exogenous ABA concentration gradient, however there is no variation between types on the sensitivity to it. Also, both cypselae types were indifferent to Fluridone (ABA inhibitor), which indicates that the dormancy is not maintained by de novo ABA synthesis. Cypselae types had different sensitivity to an exogenous GA3 gradient, the central type being more sensitive to the treatment than the peripheral one. But when the endogenous GA synthesis was blocked by Paclobutrazol, both types responded equally to same GA3 concentrations. This indicates that endogenous GA synthesis may be related to differences observed on germination of cypselae types. To conclude, seed types differ on their growth potential to overcome the pericarp resistance: while the inhibitor in the peripheral pericarp reduces growth potential, GA increases it. Resumo Bidens pilosa L. é uma espécie de planta daninha heterocarpica com dois tipos de cipselas que possuem diferenças morfofisiológicas, sendo o tipo periférico de menor tamanho e com germinação lenta se comparado com o central. Nosso objetivo foi verificar como o mecanismo de germinação varia entre os tipos. Focamos em dois mecanismos: (1) restrição causada pelo pericarpo (física e química) e (2) estímulo hormonal (Ácido abscísico [ABA] e Giberelina [GA]). Os tipos de cipselas são fisicamente limitados pelo pericarpo, pois quando ambos os tipos de sementes são excisados há um aumento na germinação, contudo as diferenças no processo se mantém. O pericarpo do tipo periférico ainda possui inibidores que efetivamente retardam a germinação das cipselas centrais intactas. Para testar os efeitos hormonais, nós focamos no controle pelo ABA:GA. Ambas cipselas responderam ao gradiente de concentração de ABA exógeno, contudo não houve variação na sensibilidade entre os tipos. Ainda, ambos tipos de cipselas foram indiferentes à Fluoridona (inibidor de ABA), que indica que a dormência não é mantida pela nova síntese de ABA. Tipos de cipselas apresentam diferentes sensibilidades ao gradiente exógeno de GA3, com o tipo central sendo mais sensível ao tratamento que o periférico. Mas quando a síntese endógena de GA foi bloqueada pelo Paclobutrazol, ambos os tipos responderam de forma similar às concentrações de GA 3. Isso indica que a síntese de GA endógena pode estar relacionada com a diferença observada na germinação dos dois tipos de cipselas. Para concluir, os tipos de sementes diferem no potencial para superar a resistência do pericarpo, sendo o inibidor no pericarpo da cipsela periférica o redutor do potencial de crescimento, enquanto a GA aumenta esse potencial.