Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(3), P. 2470 - 2470

Published: Jan. 27, 2023

Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed human food. Developing pea core collections improves our understanding evolution may ease exploitation their genetic diversity breeding programs. We carefully selected highly diverse collection 325 accessions established population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, which 24,279 were SilicoDArT 11,511 SNP markers. More than 90% these markers mapped onto reference genome, with an average 2787 1644 per chromosome, LD50 distance 0.48 1.38 Mbp, respectively. The clustered three or six subpopulations depending on subspecies. Many admixed also detected, confirming frequent exchange between populations. Our results support classification Pisum genus into two species, P. fulvum sativum (including subsp. sativum, arvense, elatius, humile, jomardii abyssinicum). In addition, study showed that wild alleles incorporated through intermediate arvense during domestication, have important implications for high found marker coverage expected to improve trait discovery efficient implementation advanced approaches.

Language: Английский

---

Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(2), P. 419 - 439

Published: Jan. 21, 2022

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi selection in natural systems. Investigating domestication may give insights into how plants react different intensities human manipulation, which has direct implication for continuing efforts crop improvement. Therefore, scientists various disciplines study domestication-related questions understand biological and cultural bases process. We employed restriction site-associated DNA sequencing (RAD-seq) 494 Pisum sativum (pea) samples from all wild domesticated groups analyze genetic structure collection. Patterns ancient admixture were investigated by analysis graphs. two complementary approaches, one diversity based on differentiation, detect signatures putatively associated with domestication. An subpopulation P. revealed five distinct notable geographic pattern. abyssinicum clustered unequivocally within complex, without any indication hybrid origin. detected 32 genomic regions subjected selection: 29 ssp. three abyssinicum. The did not share under display similar haplotype patterns those regions. Wild structured well-diverged subgroups. Although humile supported as taxonomic entity, so-called 'southern humile' genuine group. Introgression shape variation observed sampled germplasm. pea domestication, suggesting genetically independent events.

Language: Английский

---

New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.)

Diversity, Journal Year: 2023, Volume and Issue: 15(2), P. 216 - 216

Published: Feb. 2, 2023

Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid mitochondrial genomes Pisum sativum subsp. elatius fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most peas from continental southern Europe a single specimen Morocco were found to share same organellar genome constitution; four others, presumably hybrid constitutions, Mediterranean islands Athos Peninsula. A closely related abyssinicum, Yemen Ethiopia, was unexpectedly an accession P. Israel, their being unrelated. Phylogenetic reconstructions based on different sets be most cultivated sativum, making its progenitor origin area enigmatic. An representing ‘fulvum-b’ branch, according nuclear marker, appeared branch other accessions trees. The results stress complicated evolution structure genetic diversity

Language: Английский

---

Multiple origin of organellar genomes of cultivated pea (Pisum sativum L. subsp. sativum)

Plant Gene, Journal Year: 2025, Volume and Issue: 42, P. 100492 - 100492

Published: Feb. 2, 2025

Language: Английский

---

Demographic and conservation genomic assessment of the threatened marbled teal (Marmaronetta angustirostris)

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(5)

Published: May 1, 2024

Abstract Genetic assessment of species that have experienced dramatic population declines provides critical information is instrumental for the design conservation recovery programs. Here, we use different sources molecular data (mtDNA and ddRAD‐seq) to evaluate genetic status wild captive populations marbled teal ( Marmaronetta angustirostris ), a duck classified as critically endangered in Spain near threatened at global scale. First, determined evolutionary demographic trajectories from currently much larger Iraq, which also documented source European zoo stocks. Second, evaluated suitability ongoing restocking programs assessed their potential impact on composition populations. Populations Iraq were assigned distinct clusters, albeit with an overall low level differentiation, line recent divergence (<8000 years ago) lack phylogeographic structure species. Demogenomic inferences revealed two parallel trajectories, marked bottleneck during last glacial period followed by sudden expansion stability since onset Holocene. The presented high levels inbreeding, but found no evidence bottlenecks compatible human‐driven decline past century. Spanish centers involved showed introgression zoos; however, limited stock into Spain, suggesting captive‐bred birds breeding success wild. Our study illustrates how ex situ should consider distinctiveness when establishing stocks highlights importance genetically assessing prior reinforcement actions.

Language: Английский

---

Genomic prediction and allele mining of agronomic and morphological traits in pea (Pisum sativum) germplasm collections

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Dec. 22, 2023

Well-performing genomic prediction (GP) models for polygenic traits and molecular marker sets oligogenic could be useful identifying promising genetic resources in germplasm collections, setting core establishing variety distinction. This study aimed at (i) defining GP key predicting 15 agronomic or morphological (ii) verifying the model usefulness also selection breeding programs, (iii) investigating consistency between phenotypic diversity patterns, (iv) regions associated with to target traits. The was based on phenotyping data over 41,000 genotyping-by-sequencing-generated SNP markers of 220 landraces old cultivars belonging a world collection 11 modern cultivars. Non-metric multi-dimensional scaling (NMDS) an analysis population structure indicated high level differentiation material from Western Asia, major West-East gradient, quite limited improved germplasm. Mantel’s test revealed low correlation ( r = 0.12) diversity, which increased 0.45) when considering only relative significant SNPs genome-wide association analyses. These analyses identified, inter alia, several areas chromosome 6 involved largely pleiotropic control vegetative reproductive organ pigmentation. We found various grain straw yield under severe drought onset flowering, one 5 protein content. displayed moderately predictive ability (0.43 0.61) content, yield, (0.76) individual seed weight, intra-population, intra-environment cross-validations. inter-population, inter-environment assessment trained three recombinant inbred line (RIL) populations, challenged by much narrower material, eight-fold less available different environments, led overall loss about 40% 50% content 60% no yield. Within-RIL differed among populations.

Language: Английский

---

Natural range, habitats and populations of wild peas (Pisum L.)

Genetic Resources and Crop Evolution, Journal Year: 2023, Volume and Issue: 70(4), P. 1051 - 1083

Published: Feb. 18, 2023

Language: Английский

---

Climate change conditions the selection of rust-resistant candidate wild lentil populations for in situ conservation

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 3, 2022

Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become priority in the face climate change. Bizarrely, situ conserved CWR populations and traits one might wish preserve them themselves vulnerable In this study, we used quantitative machine learning predictive approach project resistance lentils common disease, lentil rust, caused by fungus Uromyces viciae-fabae. Resistance is measured through proxy value, DSr (Disease Severity relative), quite complex expensive get. Therefore, convenient tool predict magnitude using well-curated georeferenced calibration set. Previous works have provided binary outcome (resistant vs. non-resistant), but not fine enough answer three practical questions: which variables key rust resistance, resistant under current environmental conditions, likely keep trait different change scenarios. We first present time for crop wild relatives grow up inside protected areas. Then, use same models future IPCC (Intergovernmental Panel on Climate Change) scenarios values. Populations rust-resistant now conditions optimal candidates further evaluation trait. found rust-resistance variation as result uniform across geographic scope study (the Mediterranean basin), candidate share some interesting conditions.

Language: Английский

---

Genetic structure and ecological niche space of lentil's closest wild relative, Lens orientalis (Boiss.) Schmalh.

Plant Biology, Journal Year: 2024, Volume and Issue: 26(2), P. 232 - 244

Published: Jan. 17, 2024

Abstract Crops arose from wild ancestors and to understand their domestication it is essential compare the cultivated species with crop relatives. These represent an important source of further improvement, in particular relation climate change. Although there are about 58,000 Lens accessions held genebanks, only 1% wild. We examined geographic distribution genetic diversity lentil's immediate progenitor L. orientalis . used Genotyping by Sequencing (GBS) identify characterize differentiation among at germplasm collections. then determined whether genetically distinct clusters had been collected climatically locations. Of 195 genotyped accessions, 124 were genuine four identified groups. environmental distance matrix was significantly correlated a Mantel test, not found occupy different space. Maxent modelling gave predicted pattern centred Fertile Crescent, intermediate probabilities occurrence parts Turkey, Greece, Cyprus, Morocco, south Iberian Peninsula NW Africa. Future projections did show any dramatic alterations according change scenarios tested. have considerable , some which track climatic variability. The results study showed lentil indicate importance ongoing collections situ conservation for our future capacity harness variation progenitor.

Language: Английский

---

Genomic and common garden data reveal significant genetic differentiation in the endangered San Fernando Valley spineflower Chorizanthe parryi var. fernandina

Conservation Genetics, Journal Year: 2024, Volume and Issue: 25(4), P. 879 - 896

Published: March 26, 2024

Abstract San Fernando Valley spineflower ( Chorizanthe parryi var. fernandina [S. Watson] Jeps.) (Polygonaceae) is an herbaceous annual plant, endemic to California, and until rediscovered in 1999 had been thought be extinct for almost seven decades. Historically documented at 10 locations, it currently persists 2, separated by approximately 27 km. State listed as endangered, a description of its genetic diversity structure conservation interest. After determining lack variation ploidy, we examined from samples within both populations: common garden study potentially adaptive selected growth phenological traits analysis single nucleotide polymorphisms identified through restriction-site associated DNA sequencing. Both measures indicated that this highly restricted taxon nevertheless harbors substantial levels has significant between- within-population structure. Combining approaches population genomics studies provided more insight into the patterns basis than typical non-model species. Although local adaptation was not specifically studied (i.e., via reciprocal transplant studies), differences determined these two independent lines evidence indicate mixing gene pools between populations recommended time. Further, with revealed among subpopulations, caution against genotypes across subpopulations most part, without much would pose risk outbreeding depression. The importance supporting pollinator health highlighted. With diversity—particularly species—being dynamic, fluctuating usual processes contributions soil seedbank, recommend periodic resampling monitor Climate change anticipated contribute variability.

Language: Английский

---