Kale (
Brassica oleracea.
var.
acephala
) is a nutrient-rich green leafy vegetable consumed as food and used in traditional medicine worldwide. An essential step in describing the available genetic ...resources and ensuring their effective use in breeding programs is to characterize the genetic diversity of available germplasm. In this study, the genetic diversity and structure of 26 kale accessions from South-East Europe were examined using 26 agro-morphological traits collected in the field and 12 simple sequence repeat (SSR) markers. Considerable agro-morphological variability was found in most quantitative (CV = 17.26–42.42%) and qualitative (H' = 0.61–1.79) traits. Multifactorial analysis (MFA) showed that country of origin (33.01%) and morphotype (32.30%) significantly influenced kale diversification. Leaf blade shape (20.62%), leaf incision (19.43%), anthocyanin distribution (16.43%), and leaf colour (15.55%) were the traits that most clearly differentiated accessions. The three common commercial kale cultivars were identified as independent outliers that differed from the other kale accessions in both MFA and UPGMA clustering analysis. The SSR markers were highly informative with 108 alleles and polymorphic information content ranging from 0.395 to 0.856. Strong genetic diversity was detected at the accession level (H' = 0.58) while genetic differentiation was low (Fst = 0.05). Similar to UPGMA clustering, Bayesian clustering suggests that the kale collection can be divided into four clusters with a high degree of admixture and no geographic grouping pattern is apparent. Overall, the study showed that the kale collection studied represents a valuable reservoir of genetic and agro-morphological variability that could be used for future breeding initiatives.
Seed and pollen dispersal shape patterns of gene flow and genetic diversity in plants. Pollen is generally thought to travel longer distances than seeds, but seeds determine the ultimate location of ...gametes. Resolving how interactions between these two dispersal processes shape microevolutionary processes is a long‐standing research priority. We unambiguously isolated the separate and combined contributions of these two dispersal processes in seedlings of the animal‐dispersed palm Oenocarpus bataua to address two questions. First, what is the spatial extent of pollen versus seed movement in a system characterized by long‐distance seed dispersal? Second, how does seed dispersal mediate seedling genetic diversity? Despite evidence of frequent long‐distance seed dispersal, we found that pollen moves much further than seeds. Nonetheless, seed dispersal ultimately mediates genetic diversity and fine‐scale spatial genetic structure. Compared to undispersed seedlings, seedlings dispersed by vertebrates were characterized by higher female gametic and diploid seedling diversity and weaker fine‐scale spatial genetic structure for female gametes, male gametes and diploid seedlings. Interestingly, the diversity of maternal seed sources at seed deposition sites (Nem) was associated with higher effective number of pollen sources (Nep), higher effective number of parents (Ne) and weaker spatial genetic structure, whereas seed dispersal distance had little impact on these or other parameters we measured. These findings highlight the importance maternal seed source diversity (Nem) at frugivore seed deposition sites in driving emergent patterns of fine‐scale genetic diversity and structure.
Traditional rice varieties grown by the farmers serve as valuable genetic resources for future rice improvement. These varieties are highly adapted to varied agro-ecological conditions. However, they ...are rapidly lost because of the adoption of high-yielding varieties. The extent of allelic and genetic diversity present in the germplasm is a prerequisite for the improvement of any crop and conservation strategies under adverse impacts of climate. Farmers' rice varieties are usually poor yielders but are allelic treasurer for different traits, especially biotic and abiotic stresses, grain qualities, early seedling vigor, input use efficiency, etc. Therefore, the present study was aimed for a detailed understanding of allelic and genetic diversity, and population structure of 607 farmers' rice varieties using 36 fluorescently labeled microsatellite markers and 53 morphological traits. A total of 363 alleles was detected with an average of 10.33 alleles per locus and moderately high Nei's allelic/gene diversity (0.502) was detected. Polymorphic information content ranged from 0.685 to 0.987 with an average of 0.901. 34 unique, 236 rare, 84 low-frequency and 44 high-frequency alleles were detected. 53 morphological traits harbored a total of 195 variables with an average of 4.217 variables per trait. 50 out of 53 morphological traits showed polymorphism and highly significant differences among varieties. High genetic diversity was observed among 607 farmers' rice varieties both at molecular (0.653) and phenotypic (0.656) levels. The dendrogram based on both microsatellite markers and morphological traits grouped the 607 farmers' rice varieties into three major groups. A moderate population structure was observed with two independent subpopulations SP1 and SP2, which have membership percentages of 82.6 % and 17.4 %, fixation index values of 0.19 and 0.194, respectively. The AMOVA could explain 63 % of the total variation among varieties and 34 % within varieties. Our results showed that the farmers' rice varieties of Odisha harbored higher levels of both allelic and genetic diversity. Hence, these varieties would be useful for the identification of novel and elite alleles, and serve as a source of donors for the development of climate-smart varieties with improved grain yield and qualities, and input use efficiency, which would be sustainable in changing climate scenario conditions and improve farmers' income.
•Traditional rice varieties grown by the farmers serve as valuable genetic resources for future rice improvement.•These varieties are highly adapted to varied agro-ecological conditions. However, they are rapidly lost due to adoption of high yielding varieties.•The extent of genetic diversity present in the germplasm is a prerequisite for improvement of any crop productivity, nutritional quality and conservation strategies under adverse impacts of climate.•Farmers’ rice varieties are usually poor yielder but are allelic treasurer for different traits, especially biotic and abiotic stresses, grain qualities, input use efficiency, etc.•For a detailed understanding of allelic and genetic diversity of 607 farmers’ rice varieties of Odisha, using microsatellite markers, is crucial for development of efficient conservation strategies in the rice improvement programs
Key message
Association analysis resulted in the identification of specific
StGWD
alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and ...tetraploid potato mapping populations.
Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (
StGWD
) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two
StGWD
amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (
Ho
= 0.765). The average number of different haplotypes per individual (
Ai
) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific
StGWD
alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO
4
/mg starch to 38 nmol PO
4
/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.
Genetic diversity is considered to be a prerequisite for adaptation and adaptability as it is a key element of biological diversity. However, the monitoring of genetic diversity has tended to be ...ignored in biodiversity monitoring. We report a comprehensive genetic monitoring effort in two dominant forest tree species, which was started with a baseline survey in 12 European beech populations and 10 Norway spruce populations in Germany. The standardized experimental design is based on collecting samples of at least 250 adult trees, and 400 natural regeneration and 400 seed samples and their genotyping with 15–16 high-resolution SSR markers. In addition to commonly used mean values across the markers to quantify genetic diversity, we placed special emphasis on various marker-based, pedigree-based and demographic models for estimating the contemporary effective population size N
e
of the different generations. In both beech and spruce, no variation in genetic diversity with mean values across markers was detectable between the studied stands and between age cohorts. We detected that stable allelic diversity in progeny generations is ensured by sufficient gene flow from surrounding forests. However, estimates of effective population size show marked differentiation among populations and among age cohorts. Natural regeneration samples appear to converge on the parent generation, while seed samples show a clear bottleneck effect. The N
e
parameter can be used to derive conclusions for sustainable natural regeneration management in forest stands and for seed stand approvals including adequate seed collections for appropriate artificial regenerations.The sibship frequency-based method for N
e
estimates is presented as much more robust than the widely used LD estimates, which often fail for samples with too weak relatedness. Despite the distinct kinship structure in our monitoring plots, the contemporary effective population size proves to be an essential parameter for assessing the integrity of the reproductive system.
The TORC1 pathway coordinates cell growth in response to nitrogen availability present in the medium, regulating genes related to nitrogen transport and metabolism. Therefore, the adaptation of
...Saccharomyces cerevisiae
to changes in nitrogen availability implies variations in the activity of this signaling pathway. In this sense, variations in nitrogen detection and signaling pathway are one of the main causes of differences in nitrogen assimilation during alcoholic fermentation. Previously, we demonstrated that allelic variants in the
GTR1
gene underlying differences in ammonium and amino acids consumption between Wine/European (WE) and West African (WA) strains impact the expression of nitrogen transporters. The
GTR1
gene encodes a GTPase that participates in the EGO complex responsible for TORC1 activation in response to amino acids availability. In this work, we assessed the role of the
GTR1
gene on nitrogen consumption under fermentation conditions, using a high sugar concentration medium with nitrogen limitation and in the context of the WE and WA genetic backgrounds. The
gtr1Δ
mutant presented a reduced TORC1 activity and increased expression levels of nitrogen transporters, which in turn favored ammonium consumption, but decreased amino acid assimilation. Furthermore, to identify the SNPs responsible for differences in nitrogen consumption during alcoholic fermentation, we studied the polymorphisms present in the
GTR1
gene. We carried out swapping experiments for the promoter and coding regions of
GTR1
between the WE and WA strains. We observed that polymorphisms in the coding region of the WA
GTR1
gene are relevant for TORC1 activity. Altogether, our results highlight the role of the
GTR1
gene on nitrogen consumption in
S. cerevisiae
under fermentation conditions.
Background: STMS markers and morphological traits were used to investigate the genetic relationship and allelic diversity in chickpea. In this study, we focused on the selection and more efficient ...utilization of core germplasm in breeding programs for chickpea crop improvement using STMS and quantitative / morphological traits.
Methods: Seeds of elite accessions of chickpea were obtained from ICRISAT, Patancheru, Andhra Pradesh, India. 50 STMS markers and 11 quantitative traits were used for exploring the genetic variability and relationship in 35 chickpea accessions.
Result: A total of 97 alleles were produced out of the 32 polymorphic STMS loci with an average of 3.03 alleles per locus ranging between 2-6 alleles per primer. The PIC value ranged from 0.029 to 0.768 with an average of 0.502. PIC value showed a highly positive correlation (r = 0.718) with number of alleles at the STMS loci. In both molecular and morphological markers / traits-based clustering, out of 35 chickpea accessions only one accession ICC-13892 was isolated at the end of clustering. The results indicated that highly polymorphic microsatellite markers NCPGR 68, NCPGR 50, NCPGR 81, NCPGR 48 and NCPGR 77 along with the accessions ICC-13892 having distant associations with ICC-13816, ICC-15697, ICC-15610, ICC-15868, ICC-15888, ICC-15996 with novel findings should be useful resources for strategies of allele mining, association genetics, mapping and cloning of gene(s) and in applied breeding to broaden the genetic base of chickpea.
Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of ...heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.
The study involved evaluation of 96 wheat genotypes for early maturity and related traits and molecular characterization of trait specific candidate genotypes using 26 (20 random and 6 genic) SSR ...markers. Trait characterization revealed significant variation for early maturity and other related traits. The analysis of genotypic data of 26 markers led to the detection of 166 alleles ranging from 2 to 8 alleles with an average of 3.8 alleles per locus. Separate analysis of genotypic data of 20 random and 06 trait specefic markers led to the identification of 118 and 51 alleles, respectively. Allelic diversity study in the two sub-populations i.e., early and late maturing populations detected a total of 167 and 144 alleles, respectively. Higher gene diversity was detected in early maturing sub-population (0.135) when compared to late maturing sub-population (0.071). Single marker analysis revealed significant association of 05 random (
Xcfd31, Xcfd39, Xgwm148, Xgwm190
and
Xgwm538
) and 02 trait specific markers (
Xwmc1
and
Xgwm271
) with early maturity. Therefore, two trait specific markers explaining 21.36% and 10.94% phenotypic variation (PVE%) respectively for early maturity are declared validated during the present study. Overall, the findings of the present study will prove useful in future wheat improvement programs aimed at developing early maturing wheat varieties.
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