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Genetic Diversity of Potato Cultivars for Nitrogen Use Efficiency Under Contrasting Nitrogen Regimes
Getahun, Baye Berihun ; Kassie, Molla Mekonen ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2019
Potato Research (2019). - ISSN 0014-3065
Dutch potato cultivars - Ethiopian potato cultivars - Genetic diversity - Nitrogen use efficiency - Path coefficient analysis
Developing cultivars that use nitrogen more efficiently is a sustainable strategy for reducing nitrogen use in crop production. To assess the genetic diversity for nitrogen use efficiency (NUE) and related traits in potato, a total of 97 (88 for the Western-European market and 9 Ethiopian) cultivars were evaluated at two nitrogen levels (40 kg/ha and 120 kg/ha) for 24 quantitative traits in Debre-Tabor and Injibara (Ethiopia) in the 2013 main rainy season (June to September). Highly significant variation was found among genotypes for almost all measured traits. Plant height, NUE, tuber yield, and yield-related traits and model parameters for canopy development (maximum canopy covers area under the canopy curve) were significantly affected by N levels across locations. Dutch cultivars had more rapid initial canopy development and matured earlier than the Ethiopian cultivars at both N levels and locations. A hierarchical cluster analysis grouped the cultivars in 9 and 11 genetically distinct classes at low and high N, respectively. The genetic component accounted for a large portion of the phenotypic variation for plant height, tuber number per plant, average tuber weight, and NUE under both N regimes, as indicated by a high heritability. Strong phenotypic correlations were observed between NUE and tuber number per plant, days to maturity, tuber dry matter %, maximum canopy cover, and area under the canopy curve under both low and high N conditions. The result is indicative to set the best parental line selection criteria for crossing purpose and utilize the cultivars for further potato NUE breeding programmes.
Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods
Winter, Iris I. de; Qurkhuli, Tamar ; Groot, Nanine de; Vos-Rouweler, Annemiek J.M. de; Hooft, Pim van; Heitkönig, Ignas M.A. ; Prins, Herbert H.T. ; Bontrop, Ronald E. ; Doxiadis, Gaby G.M. - \ 2019
Immunogenetics 71 (2019)2. - ISSN 0093-7711 - p. 97 - 107.
Balancing selection - Eulemur - Genetic diversity - Major histocompatibility complex - Polymorphism
The major histocompatibility complex (MHC) is a highly polymorphic and polygenic genomic region that plays a crucial role in immune-related diseases. Given the need for comparative studies on the variability of immunologically important genes among wild populations and species, we investigated the allelic variation of MHC class II DRB among three congeneric true lemur species: the red-fronted lemur (Eulemur rufifrons), red-bellied lemur (Eulemur rubriventer), and black lemur (Eulemur macaco). We noninvasively collected hair and faecal samples from these species across different regions in Madagascar. We assessed DRB exon 2 polymorphism with a newly developed primer set, amplifying nearly all non-synonymous codons of the antigen-binding sites. We defined 26 DRB alleles from 45 individuals (17 alleles from E. rufifrons (N = 18); 5 from E. rubriventer (N = 7); and 4 from E. macaco (N = 20). All detected alleles are novel and show high levels of nucleotide (26.8%) and non-synonymous codon polymorphism (39.4%). In these lemur species, we found neither evidence of a duplication of DRB genes nor a sharing of alleles among sympatric groups or allopatric populations of the same species. The non-sharing of alleles may be the result of a geographical separation over a long time span and/or different pathogen selection pressures. We found dN/dS rates > 1 in the functionally important antigen recognition sites, providing evidence for balancing selection. Especially for small and isolated populations, quantifying and monitoring DRB variation are recommended to establish successful conservation plans that mitigate the possible loss of immunogenetic diversity in lemurs.
Genetic diversity of endangered terrestrial orchids Spathoglottis plicata in Peninsular Malaysia based on AFLP markers
Ginibun, Florence C. ; Arens, Paul ; Vosman, Ben ; Bhassu, Subha ; Khalid, Norzulaani ; Othman, Rofina Yasmin - \ 2018
Plant OMICS 11 (2018)3. - ISSN 1836-0661 - p. 135 - 144.
AFLP - Genetic diversity - Spathoglottis plicata - Terrestrial orchids
Spathoglottis plicata is an endangered terrestrial orchid species that have experienced severe threats to its habitat as wild forest sites come under pressure from industrialisation and natural disasters. This orchid species chosen to evaluate their levels of genetic diversity and population genetic structure, which 25-30 accession collected in the different location with different geographical, altitude and habitat. Genomic DNA was extracted from six natural populations (n=172) in Peninsular Malaysia using eleven AFLP markers of EcoRI+3 bases/MseI+3 base primer combinations. Based on 279 polymorphic bands, a significant degree of genetic population differentiation was found, with a 78.5% variation within populations as measured by AMOVA, indicating a potential restricted gene flow. Two distinct clades generated from a UPGMA dendrogram were further investigated through a Bayesian analysis using STRUCTURE software, producing an estimated population structure at optimal value K=4. These results point to the presence of four genetic structures in the Spathoglottis plicata population. The Pahang and Terengganu population revealed a higher than average genetic variation (60.25%), indicating that there may be a robust structural division between the population samples and a possible hybridisation between the Northern (Kedah), Southern (Negeri Sembilan and Johor) and Central (Selangor) region populations. In sum, these results suggest that geographical distance is the primary factor contributing to differences among populations and the need for conservation measures to protect the Spathoglottis plicata species.
Latitudinal adaptation and genetic insights into the origins of cannabis sativa L.
Zhang, Qingying ; Chen, Xuan ; Guo, Hongyan ; Trindade, Luisa M. ; Salentijn, Elma M.J. ; Guo, Rong ; Guo, Mengbi ; Xu, Yanping ; Yang, Ming - \ 2018
Frontiers in Plant Science 871 (2018). - ISSN 1664-462X
Cannabaceae - CpDNA - Genetic diversity - Industrial hemp - Phylogeography
Cannabis is one of the most important industrial crops distributed worldwide. However, the phylogeographic structure and domestication knowledge of this crop remains poorly understood. In this study, sequence variations of five chloroplast DNA (cpDNA) regions were investigated to address these questions. For the 645 individuals from 52 Cannabis accessions sampled (25 wild populations and 27 domesticated populations or cultivars), three haplogroups (Haplogroup H, M, L) were identified and these lineages exhibited distinct high-middle-low latitudinal gradients distribution pattern. This pattern can most likely be explained as a consequence of climatic heterogeneity and geographical isolation. Therefore, we examined the correlations between genetic distances and geographical distances, and tested whether the climatic factors are correlated with the cpDNA haplogroup frequencies of populations. The “isolation-by-distance” models were detected for the phylogeographic structure, and the day-length was found to be the most important factor (among 20 BioClim factors) that influenced the population structures. Considering the distinctive phylogeographic structures and no reproductive isolation among members of these lineages, we recommend that Cannabis be recognized as a monotypic genus typified by Cannabis sativa L., containing three subspecies: subsp. sativa, subsp. Indica, and subsp. ruderalis. Within each haplogroup which possesses a relatively independent distribution region, the wild and domesticated populations shared the most common haplotypes, indicating that there are multiregional origins for the domesticated crop. Contrast to the prevalent Central-Asia-Origin hypothesis of C. saltiva, molecular evidence reveals for the first time that the low latitude haplogroup (Haplogroup L) is the earliest divergent lineage, implying that Cannabis is probably originated in low latitude region.
Hytrosavirus genetic diversity and eco-regional spread in Glossina species
Meki, Irene K. ; Kariithi, Henry M. ; Ahmadi, Mehrdad ; Parker, Andrew G. ; Vreysen, Marc J.B. ; Vlak, Just M. ; Oers, Monique M. van; Abd-Alla, Adly M.M. - \ 2018
BMC Microbiology 18 (2018). - ISSN 1471-2180
Genetic diversity - Glossinidae - GpSGHV - Haplotype - Salivary gland hypertrophy virus - Sterile insect technique - Tsetse - Virus evolution
BACKGROUND: The management of the tsetse species Glossina pallidipes (Diptera; Glossinidae) in Africa by the sterile insect technique (SIT) has been hindered by infections of G. pallidipes production colonies with Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae family). This virus can significantly decrease productivity of the G. pallidipes colonies. Here, we used three highly diverged genes and two variable number tandem repeat regions (VNTRs) of the GpSGHV genome to identify the viral haplotypes in seven Glossina species obtained from 29 African locations and determine their phylogenetic relatedness. RESULTS: GpSGHV was detected in all analysed Glossina species using PCR. The highest GpSGHV prevalence was found in G. pallidipes colonized at FAO/IAEA Insect Pest Control Laboratory (IPCL) that originated from Uganda (100%) and Tanzania (88%), and a lower prevalence in G. morsitans morsitans from Tanzania (58%) and Zimbabwe (20%). Whereas GpSGHV was detected in 25-40% of G. fuscipes fuscipes in eastern Uganda, the virus was not detected in specimens of neighboring western Kenya. Most of the identified 15 haplotypes were restricted to specific Glossina species in distinct locations. Seven haplotypes were found exclusively in G. pallidipes. The reference haplotype H1 (GpSGHV-Uga; Ugandan strain) was the most widely distributed, but was not found in G. swynnertoni GpSGHV. The 15 haplotypes clustered into three distinct phylogenetic clades, the largest contained seven haplotypes, which were detected in six Glossina species. The G. pallidipes-infecting haplotypes H10, H11 and H12 (from Kenya) clustered with H7 (from Ethiopia), which presumably corresponds to the recently sequenced GpSGHV-Eth (Ethiopian) strain. These four haplotypes diverged the most from the reference H1 (GpSGHV-Uga). Haplotypes H1, H5 and H14 formed three main genealogy hubs, potentially representing the ancestors of the 15 haplotypes. CONCLUSION: These data identify G. pallidipes as a significant driver for the generation and diversity of GpSGHV variants. This information may provide control guidance when new tsetse colonies are established and hence, for improved management of the virus in tsetse rearing facilities that maintain multiple Glossina species.
Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars
Öztürk, Süleyman Can ; Göktay, Mehmet ; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne - \ 2018
Plant Molecular Biology Reporter 36 (2018)5-6. - ISSN 0735-9640 - p. 800 - 811.
Barcode - Filbert genomic SSRs - Fingerprinting - Genetic diversity - Illumina sequencing - Microsatellites - Population structure
European hazelnut (Corylus avellana) is a diploid tree species and is widely used in confections. Hazelnuts are, to a large part, produced in Turkey with the cultivar “Tombul” widely grown in the Black Sea region. In this work, the “Tombul” genome was partially sequenced by next-generation sequencing technology yielding 29.2% (111.85 Mb) of the ~ 385 Mb (1C). This sequence information was used to develop genetic markers in order to enable differentiation of material before the long maturation process and to facilitate future breeding strategies. A total of 90,142 simple sequence repeats (SSRs) were identified in the contigs giving a frequency of 1 SSR per 1240 nt in the assembly. Mononucleotides were the most abundant SSR marker type (60.9%) followed by di- and trinucleotides. Primer pairs were designed for 75,139 (83.3%) of the SSRs. Fifty SSR primers were applied to 47 hazelnut accessions from nine countries to test their effectiveness and polymorphism. The markers amplified an average of 3.2 fragments. The highest polymorphism information content value was for cavSSR11062 (0.97) and the lowest (0.04) was for cavSSR13386. Two markers were monomorphic: cavSSR12855 and cavSSR13267. Single-copy SSR primers were also assessed for their ability to discriminate 19 Turkish cultivars, and it was found that seven primer pairs (Cav4217, Cav14875, Cav14418, Cav2704, Cav12862, Cav3909, Cav1361) were sufficient for this task. Thus, this study developed new SSR markers for use in hazelnut breeding and genetic studies and also provide a method to distinguish and identify true-type Turkish cultivars.
Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds
Onzima, Robert B. ; Upadhyay, Maulik R. ; Doekes, Harmen P. ; Brito, Luiz F. ; Bosse, Mirte ; Kanis, Egbert ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. - \ 2018
Frontiers in Genetics Livestock Genomics 9 (2018). - ISSN 1664-8021
Adaptation - Candidate genes - Capra hircus - Genetic diversity - Genomic inbreeding - Homozygosity - Selective sweeps
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
Plant breeding and diversity : A troubled relationship?
Louwaars, Niels P. - \ 2018
Euphytica 214 (2018)7. - ISSN 0014-2336
Biodiversity policy - Diversity bottleneck - Genetic diversity - Genetic resources - Multiline - Nagoya Protocol - Participatory plant breeding - Plant breeding - Seed regulations - Trait breeding
Plant breeding collects, induces and rearranges genetic diversity followed by selection. Breeding may contribute to diversity in farmers’ fields or significantly reduce it. History has numerous examples of both. The diversity of many crops have gone through domestication, dispersal and modernization bottlenecks. Between these major decreasing processes, diversity has picked up through different evolutionary processes, and plant breeding affected by policies. Major negative effects of plant breeding on diversity have been recorded following the modernization bottleneck, but alternative breeding strategies have come up as well, both in the formal system and in the interphase between formal and farmers’ seed systems. Multiline breeding and participatory plant breeding are introduced as examples to also analyse effects of current developments in technology and policy. This paper intends to shed some light on the questions: how will current developments in technology and policy affect crop genetic diversity? Are we heading for a new bottleneck—either a molecular or a policy bottleneck, or a combination of both? Or could the future become more diverse? We look at the relationship between breeding, policies, and crop genetic diversity in farming systems with a birds-eye view. Notably because of current policy trends we warn for a new diversity bottleneck.
The impact of using old germplasm on genetic merit and diversity - A cattle breed case study
Eynard, Sonia E. ; Windig, Jack J. ; Hulsegge, Ina ; Hiemstra, Sipke Joost ; Calus, Mario P.L. - \ 2018
Journal of Animal Breeding and Genetics 135 (2018)4. - ISSN 0931-2668 - p. 311 - 322.
Ex-situ conservation - Gene bank - Genetic diversity - Genetic merit
Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long-term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse-Rhine-Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long-term maintenance and selection of breeds.
Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs
Eynard, Sonia E. ; Croiseau, Pascal ; Laloë, Denis ; Fritz, Sebastien ; Calus, Mario P.L. ; Restoux, Gwendal - \ 2018
G3 : Genes Genomes Genetics 8 (2018)1. - ISSN 2160-1836 - p. 113 - 121.
Genetic diversity - Genomic selection - GenPred - Optimal contribution - Reference population - Shared data resources
Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.
Low intraspecific genetic diversity indicates asexuality and vertical transmission in the fungal cultivars of ambrosia beetles
Peppel, L.J.J. van de; Aanen, D.K. ; Biedermann, P.H.W. - \ 2018
Fungal Ecology 32 (2018). - ISSN 1754-5048 - p. 57 - 64.
Ambrosia fungus - Ambrosiella - Anisandrus - Asexuality - Clonal fungiculture - Genetic diversity - Symbiosis - Vertical transmission - Xylosandrus
Ambrosia beetles farm ascomycetous fungi in tunnels within wood. These ambrosia fungi are regarded asexual, although population genetic proof is missing. Here we explored the intraspecific genetic diversity of Ambrosiella grosmanniae and Ambrosiella hartigii (Ascomycota: Microascales), the mutualists of the beetles Xylosandrus germanus and Anisandrus dispar. By sequencing five markers (ITS, LSU, TEF1α RPB2, β-tubulin) from several fungal strains, we show that X. germanus cultivates the same two clones of A. grosmanniae in the USA and in Europe, whereas A. dispar is associated with a single A. hartigii clone across Europe. This low genetic diversity is consistent with predominantly asexual vertical transmission of Ambrosiella cultivars between beetle generations. This clonal agriculture is a remarkable case of convergence with fungus-farming ants, given that both groups have a completely different ecology and evolutionary history.
Genetic traits of relevance to sustainability of smallholder sheep farming systems in South Africa
Molotsi, Annelin ; Dube, Bekezela ; Oosting, Simon ; Marandure, Tawanda ; Mapiye, Cletos ; Cloete, Schalk ; Dzama, Kennedy - \ 2017
Sustainability 9 (2017)8. - ISSN 2071-1050
Animal breeding - Economic indicators - Environmental indicators - Genetic diversity - Robustness - Social indicators
Sustainable livestock production is important to ensure continuous availability of resources for future generations. Most smallholder livestock farming systems in developing countries have been perceived to be environmentally, socially and economically unsustainable. Farming with livestock that is robust and adaptable to harsh environments is important in developing countries especially in semi-arid and arid environments. This review discusses the different sheep farming systems employed by smallholder farmers and associated sustainability problems facing them. The review also gives an overview of sustainability indicators and limitations to the sustainability for the different smallholder sheep production systems in South Africa. It is argued that genetic diversity is important for sustainability and needs to be maintained in sheep for sustainable production and reproduction performance. The application of traditional breeding and genomics to ensure sustainable production is explored. Animal breeding approaches, specifically genomics can be applied to improve areas of environmental sustainability of smallholder sheep farming systems but must be targeted to the specific production environments, challenges, and opportunities of smallholder production. The genetic traits important for sustainability, the role of genomics in improving these traits and linking these genetic traits to different farming systems in South Africa are discussed.
Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account
Hulsegge, B. ; Calus, M.P.L. ; Oldenbroek, J.K. ; Windig, J.J. - \ 2017
Journal of Animal Breeding and Genetics 134 (2017)1. - ISSN 0931-2668 - p. 69 - 77.
Conservation - Genetic diversity - Population structure - Relationships with other breeds
From a genetic point of view, the selection of breeds and animals within breeds for conservation in a national gene pool can be based on a maximum diversity strategy. This implies that priority is given to conservation of breeds and animals that diverge most and overlap of conserved diversity is minimized. This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions to the genetic diversity in DFR. One of these lines comprises unique diversity both within the breed and across all cattle breeds. The other line comprises unique diversity for the DFR but overlaps with the Holstein Friesian breed. There seems to be no necessity to conserve the other five lines separately, because their level of differentiation is very low. This study illustrates that, when taking conservation decisions for a breed, it is worthwhile to take into account the population structure of the breed itself and the relationships with other breeds.
After genome-wide association studies : Gene networks elucidating candidate genes divergences for number of teats across two pig populations
Verardo, L.L. ; Lopes, M.S. ; Wijga, S. ; Madsen, O. ; Silva, F.F. ; Groenen, M.A.M. ; Knol, E.F. ; Lopes, P.S. ; Guimarães, S.E.F. - \ 2016
Journal of Animal Science 94 (2016)4. - ISSN 0021-8812 - p. 1446 - 1458.
Complex trait - Genetic diversity - Genomewide association study
Number of teats (NT) is an important trait affecting both piglet’s welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. Therefore, gene networks derived from genomewide association study (GWAS) results can be used to examine shared pathways and functions of putative candidate genes. Besides, such analyses may also be helpful to understand the genetic diversity between populations for the same trait or traits. In this study, we identified significant SNP for Landrace-based (line C) and Large White–based (line D) dam lines. Besides, gene– transcription factor (TF) networks were constructed aiming to obtain the most likely candidate genes for NT in each line followed by a comparative analysis between both lines to access similarities or dissimilarities at the marker and gene level. We identified 24 and 19 significant SNP (Bayes factor ≥ 100) for lines C and D, respectively. Only 1 significant SNP overlapped both lines. Network analysis illustrated gene interactions consistent with known mammal’s breast biology and captured known TF. We observed different sets of putative candidate genes for NT in each line evaluated that may have common effects on the phenotype. Based on these results, we demonstrated the importance of post-GWAS analyses increasing the biological understanding of relevant genes for a complex trait. Moreover, we believe that this genomic diversity across lines should be taken into account, considering breed-specific reference populations for genomic selection.