Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. (Résumé d'auteur

Chloroplast Sequence of Treegourd (Crescentia cujete, Bignoniaceae) to Study Phylogeography and Domestication

Premise of the study: Crescentia cujete (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs). Methods and Results: Using a genome skimming approach, the whole chloroplast of C. cujete was assembled using 3,106,928 sequence reads of 150 bp. The chloroplast is 154,662 bp in length, structurally divided into a large single copy region (84,788 bp), a small single copy region (18,299 bp), and two inverted repeat regions (51,575 bp) with 88 genes annotated. By resequencing the whole chloroplast, we identified 66 SNPs in C. cujete (N = 30) and 68 SNPs in C. amazonica (N = 6). Nucleotide diversity was estimated at 1.1 × 10-3 and 3.5 × 10-3 for C. cujete and C. amazonica, respectively. Conclusions: This broadened C. cujete genetic toolkit will be important to study the origin, domestication, diversity, and phylogeography of treegourds in the Neotropics. © 2016 Moreira et al. Published by the Botanical Society of America

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as “adaptive introgression”. Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers’ knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics. Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes. Both of these approaches have some limitations, therefore alternative resources for the genetic dissection of complex traits continue to be sought. Here we describe one such alternative, the Multiparent Advanced Generation Inter-Cross (MAGIC). This approach is expected to improve the precision with which QTL can be mapped, improving the outlook for QTL cloning. Here, we present the first panel of MAGIC lines developed: a set of 527 recombinant inbred lines (RILs) descended from a heterogeneous stock of 19 intermated accessions of the plant Arabidopsis thaliana. These lines and the 19 founders were genotyped with 1,260 single nucleotide polymorphisms and phenotyped for development-related traits. Analytical methods were developed to fine-map quantitative trait loci (QTL) in the MAGIC lines by reconstructing the genome of each line as a mosaic of the founders. We show by simulation that QTL explaining 10% of the phenotypic variance will be detected in most situations with an average mapping error of about 300 kb, and that if the number of lines were doubled the mapping error would be under 200 kb. We also show how the power to detect a QTL and the mapping accuracy vary, depending on QTL location. We demonstrate the utility of this new mapping population by mapping several known QTL with high precision and by finding novel QTL for germination data and bolting time. Our results provide strong support for similar ongoing efforts to produce MAGIC lines in other organisms

A Set of 100 Chloroplast DNA Primer Pairs to Study Population Genetics and Phylogeny in Monocotyledons

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies

Structure et dynamique de la diversité d'une plante cultivée à multiplication végétative : le cas des ignames au Bénin (Dioscorea sp.)

We studied how farmers' practices contribute to the dynamics and the structure of the diversity of a vegetatively propagated crop, yam (Dioscorea sp.) in Benin. First, we showed the diploidy of the studied species (D. rotundata, D. abyssinica and D. praehensilis). We analysed gene flows between wild (D. abyssinica and D. praehensilis) and cultivated (D. rotundata) species. First, we showed the existence and the viability of inter-specific hybrids. Then, we showed that through the ennoblement practice, some farmers create new varieties from wild plants, inter-specific hybrids and probably from inter-varietal hybrids. Farmers thus use the sexual reproduction of wild and cultivated yams and maintain evolutionary processes in this vegetatively propagated crop. We then analysed the diversity of the cultivated species and its structure at village level. Our results suggest that yam varieties were created from products of sexual reproduction. Varieties are polyclonal but genetically homogeneous. Indeed, this diversity is interpreted as mutants that derived from the same genotype. Lastly, farmers cultivate the same variety group and exchange tubers, which explains the lack of differentiation observed between the genetic pools cultivated by different farmers.Nous avons étudié comment les pratiques paysannes contribuent à la dynamique et la structuration de la diversité d'une plante cultivée à multiplication végétative, l'igname (Dioscorea sp.) au Bénin. Dans un premier temps, nous avons montré la diploïdie des espèces étudiées (D. rotundata, D. abyssinica et D. praehensilis). Nous avons mis en évidence des flux de gènes entre les compartiments sauvage (D. abyssinica et D. praehensilis) et cultivé (D. rotundata). Tout d'abord, nous avons montré l'existence et la viabilité d'hybrides interspécifiques. Puis, nous avons montré qu'à travers la pratique de l'ennoblissement, certains paysans créent de nouvelles variétés à partir d'individus sauvages, d'hybrides interspécifiques et probablement à partir d'hybrides inter-variétaux. Les paysans utilisent donc la reproduction sexuée des ignames sauvages et cultivées et participent ainsi à maintenir les processus évolutifs chez cette plante à multiplication végétative. Nous avons ensuite analysé la diversité du compartiment cultivé et son organisation à l'échelle d'un village. Nos résultats suggèrent que les variétés d'ignames ont été créées à partir de produits de reproduction sexuée. Les variétés sont polyclonales mais homogènes génétiquement. En effet, cette diversité s'interprète comme des mutants dérivant d'un même génotype. Enfin, les agriculteurs cultivent les mêmes groupes de variétés et échangent des tubercules entre eux, ce qui conduit à une absence de différenciation entre les pools génétiques cultivés par les différents paysans

Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis

The role of standing genetic variation in adaptive evolution remains unclear. Although there has been much progress in identifying candidate genes that underlie adaptive traits, we still lack direct evidence that natural allelic variation in these genes can actually mediate adaptive evolution. In this study, we investigate the role of natural allelic variation in two candidate flowering time genes, in response to selection for early flowering in Arabidopsis thaliana: FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). We performed artificial selection for early flowering under 'spring-' and 'winter-annual' growth conditions using an outbred population of A. thaliana produced by intermating 19 natural accessions. FRI and FLC are involved in A. thaliana's response to winter conditions, and nonfunctional and weak alleles at these loci are know to reduce flowering time, particularly under spring-annual conditions. Our results provide direct evidence that natural allelic variation in FRI can provide rapid and predictable adaptive evolution in flowering time under spring-annual conditions. We observed a strong response to selection, in terms of reducing flowering time, in both growth conditions (similar to 2 standard deviation reduction). Concomitantly, the frequency of functional FRI alleles under spring-annual conditions was reduced by 68%, in agreement with predicted changes. No significant changes in allele frequencies were observed in FRI in the winter-annual growth condition or in FLC for either growth conditions. These results indicate that changes in flowering time are mediated by different genetic factors under spring- and winter-annual growth conditions, and that other loci must also be contributing to the response to selection

Structure et dynamique de la diversité d'une plante cultivée à multiplication végétative (le cas des ignames au Bénin ("Dioscorea sp."))

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