Genetic basis and timing of a major mating system shift in Capsella

YesA crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male speci-ficity components, encoded by the genesSRKandSCRat the self-incompatibility locus (S-lo-cus). Theory predicts thatS-linked mutations, and especially dominant mutations inSCR, arelikely to contribute to loss of SI. However, few studies have investigated the contribution ofdominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer speciesCapsella orientalis, by combining genetic mapping, long-read sequencing of completeS-hap-lotypes, gene expression analyses and controlled crosses. We show that loss of SI inC. orientalisoccurred<2.6 Mya and maps as a dominant trait totheS-locus. We identify a fixed frameshift deletion in the male specificity geneSCRand con-firm loss of male SI specificity. We further identify anS-linked small RNA that is predicted tocause dominance of self-compatibility. Our results agree with predictions on the contribution of dominantS-linked mutations toloss of SI, and thus provide new insights into the molecular basis of mating system transitions.Work at Uppsala Genome Center is funded by 550 RFI / VR and Science for Life Laboratory, Sweden. The SNP&SEQ Platform is supported by 551 the Swedish Research Council and the Knut and Alice Wallenberg Foundation. V.C. 552 acknowledges support by a grant from the European Research Council (NOVEL project, 553 grant #648321). The authors thank the French Ministère de l’Enseignement Supérieur et de la 554 Recherche, the Hauts de France Region and the European Funds for Regional Economical 555 Development for their financial support to this project. This work was supported by a grant 556 from the Swedish Research Council (grant #D0432001) and by a grant from the Science for 557 Life Laboratory, Swedish Biodiversity Program to T.S. The Swedish Biodiversity Program is 558 supported by the Knut and Alice Wallenberg Foundation

Successful wide hybridization and introgression breeding in a diverse set of common peppers (Capsicum annuum) using different cultivated ají (C. baccatum) accessions as donor parents

[EN] Capsicum baccatum, commonly known as aji, has been reported as a source of variation for many different traits to improve common pepper (C. annuum), one of the most important vegetables in the world. However, strong interspecific hybridization barriers exist between them. A comparative study of two wide hybridization approaches for introgressing C. baccatum genes into C. annuum was performed: i) genetic bridge (GB) using C. chinense and C. frutescens as bridge species; and, ii) direct cross between C. annuum and C. baccatum combined with in vitro embryo rescue (ER). A diverse and representative collection of 18 accessions from four cultivated species of Capsicum was used, including C. annuum (12), C. baccatum (3), C. chinense (2), and C. frutescens (1). More than 5000 crosses were made and over 1000 embryos were rescued in the present study. C. chinense performed as a good bridge species between C. annuum and C. baccatum, with the best results being obtained with the cross combination [C. baccatum (female) x C. chinense (male)] (female) x C. annuum (male), while C. frutescens gave poor results as bridge species due to strong prezygotic and postzygotic barriers. Virus-like-syndrome or dwarfism was observed in F-1 hybrids when both C. chinense and C. frutescens were used as female parents. Regarding the ER strategy, the best response was found in C. annuum (female) x C. baccatum (male) crosses. First backcrosses to C. annuum (BC(1)s) were obtained according to the crossing scheme [C. annuum (female) x C. baccatum (male)] (female) x C. annuum (male) using ER. Advantages and disadvantages of each strategy are discussed in relation to their application to breeding programmes. These results provide breeders with useful practical information for the regular utilization of the C. baccatum gene pool in C. annuum breeding.Juan P. Manzur thanks Universitat Politecnica de Valencia for a research predoctoral grant (2011-S2-4264, programa para la formacion de personal investigador). Authors are grateful to Centro Inv. Agr. Mabegondo, S. Larregla from NEIKER, P.W. Bosland from NMSU and the Consejos Reguladores of IGP Pimiento Asado del Bierzo, DOP Pimenton de Murcia, and IGP Piquillo de Lodosa for providing us with seeds from Arnoia, Guindilla de Ibarra, Numex, Bierzo, Bola and Piquillo, respectively.Manzur Poblete, JPA.; Fita, A.; Prohens Tomás, J.; Rodríguez Burruezo, A. (2015). Successful wide hybridization and introgression breeding in a diverse set of common peppers (Capsicum annuum) using different cultivated ají (C. baccatum) accessions as donor parents. PLoS ONE. 10(12). https://doi.org/10.1371/journal.pone.0144142Se0144142101

Interspecific introgression mediates adaptation to whole genome duplication

Adaptive gene flow is a consequential phenomenon across all kingdoms. While recognition is increasing, examples lack of bidirectional gene flow mediating adaptations at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of meiotic machinery controlling crossover number upon adaptation to whole genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD and that the merger of these species is greater than the sum of their parts

The Gene Pool Concept Applied to Crop Wild Relatives: An Evolutionary Perspective

Crop wild relatives (CWR) can provide important resources for the genetic improvement of cultivated species. Because crops are often related to many wild species and because exploration of CWR for useful traits can take many years and substantial resources, the categorization of CWR based on a comprehensive assessment of their potential for use is an important knowledge foundation for breeding programs. The initial approach for categorizing CWR was based on crossing studies to empirically establish which species were interfertile with the crop. The foundational concept of distinct gene pools published almost 50 years ago was developed from these observations. However, the task of experimentally assessing all potential CWR proved too vast; therefore, proxies based on phylogenetic and other advanced scientific information have been explored. A current major approach to categorize CWR aims to comprehensively synthesize experimental data, taxonomic information, and phylogenetic studies. This approach very often ends up relying not only on the synthesis of data but also intuition and expert opinion and is therefore difficult to apply widely in a reproducible manner. Here, we explore the potential for a stronger standardization of the categorization method, with focus on evolutionary relationships among species combined with information on patterns of interfertility between species. Evolutionary relationships can be revealed with increasing resolution via next-generation sequencing, through the application of the multispecies coalescent model and using focused analyses on species discovery and delimitation that bridge population genetics and phylogenetics fields. Evolutionary studies of reproductive isolation can inform the understanding of patterns of interfertility in plants. For CWR, prezygotic postpollination reproductive barriers and intrinsic postzygotic barriers are the most important factors and determine the probability of producing viable and fertile offspring. To further the assessment of CWR for use in plant breeding, we present observed and predicted gene pool indices. The observed index quantifies patterns of interfertility based on fertilization success, seed production, offspring viability, and hybrid fertility. The predicted gene pool index requires further development of the understanding of quantitative and qualitative relationships between reproductive barriers, measures of genetic relatedness, and other relevant characteristics for crops and their wild relatives

Evolution and function of epigenetic processes in the endosperm

The endosperm is an ephemeral tissue surrounding the embryo that is essential for its development. Aside from the embryo nourishing function, the endosperm serves as a battlefield for epigenetic processes that have been hypothesized to reinforce transposable element silencing in the embryo. Specifically, global DNA demethylation in the central cell may serve to produce small RNAs that migrate to egg cell and embryo to induce de novo DNA methylation. The Polycomb Repressive Complex2 (PRC2) is particularly targeted to DNA hypomethylated regions, possibly alleviating the negative effects associated with loss of DNA methylation in the endosperm. The functional requirement of the PRC2 in the endosperm can be bypassed by increasing the maternal genome dosage in the endosperm, suggesting a main functional role of the endosperm PRC2 in reducing sexual conflict. We therefore propose that the functional requirement of an endosperm PRC2 was coupled to the evolution of a sexual endosperm and mechanisms enforcing transposon silencing in the embryo. The evolutionary consequences of this scenario for genome expansion will be discussed