- Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties. - Background: Genetic improvement of pearl millet is lagging behind most of the major crops. - On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. - Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture.. - Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. - It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. - The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. - Pearl millet (Pennisetum glaucum (L.) R. - crop grown in the arid and semi-arid areas of the world.. - Pearl millet is the most widely grown millet species, ac- counting for approximately half of the total worldwide production of millets [36]. - Full list of author information is available at the end of the article Kanfany et al. - Therefore, on top of the currently estimated 41% of the land area of arid and semiarid zones considered unsuitable for crop production [30], more land is expected to become unfavorable for crop production. - Research em- phasis on climate-smart crops such as pearl millet would have significant contribution in mitigation of the negative impacts of the looming climate change on food security of the dissolute environments. - Although pearl millet is grown as a rainfed crop in a wide range of ecological zones and production systems, its yield is very low and spatially and temporally variable. - An innovative breeding strategy is required to develop improved climate-resilient pearl millet cultivars that can contribute to a sustainable food supply for the ever-increasing population [33].. - Pearl millet is also gaining a reputation as a health- promoting nutritious grain. - Previous studies have shown that pearl millet is an excellent source of micronutrients like iron and zinc [22]. - Tap- ping into this potential of pearl millet for the development of diversified foods with health benefits may provide a low- cost solution for the problems related to micronutrient defi- ciencies mainly in children and women who are entirely dependent on the crop as a staple food.. - Development of molecular markers using next-generation sequencing technology for a breeding population is a very vital tool to expedite pearl millet improvement. - Characterization of the genetic diversity and popula- tion structure of pearl millet germplasm and breeding populations is needed in order to accelerate its genetic improvement for agronomic and nutritional traits. - To- ward this goal, a panel of 309 inbred lines derived from landraces and improved open pollinated varieties col- lected from different parts of Africa and India were eval- uated for population genomics using genotyping-by- sequencing (GBS) markers. - The present investigation employed pertinent population genomic approaches to understand the extent of genetic diversity of a pearl mil- let inbred lines population comprising both potential re- storers and seed parents for hybrid variety development.. - A total of ~ 750 million total unfiltered reads were generated from 309 inbred lines arranged in four GBS plates run twice independently on an Ion Proton Next-Generation Sequen- cer (ThermoFisher Scientific, Waltham, MA, US). - Mapping the GBS reads to the pearl millet reference genome sequence initially detected 150, 977 unfiltered and non-imputed SNPs for the panel. - A total of 26,982 SNPs were mostly from the unanchored genome sequences or from the part of the genome not covered in the reference gen- ome sequence. - A high-density of high quality SNPs across the seven pearl millet chromosomes with most of the SNPs dis- tributed in the telomeric regions than the pericentro- meric regions of the chromosomes (Fig. - The kinship coefficients between pairs of the 309 inbred lines ranged from 0.00 to 1.21 with a mean value of 0.02 (Fig. - Nearly 91% of the pairwise relative kinship values were close to zero (<. - The genetic distances (GD) of pairwise comparisons of the inbred lines varied from 0.09 to 0.33 with the aver- age distance of 0.28 (Fig. - The majority of the genetic distances fell between 0.25 and 0.30. - Population structure and principal component analysis Analysis of the pearl millet inbred lines population using 30,893 LD pruned SNPs and the genetic distance matrix of the lines in ADMIXTURE [1] identified five subpopu- lations (Fig. - Each line was assigned to a group when the proportion of the membership probability was higher than 0.6.. - No cluster made exclusively of inbred lines from the same country was found. - In gen- eral, most of the lines closely related in pedigree or de- rived from landraces/improved varieties with high Fe and Zn content were grouped together, except for sub- group 2 which was formed mainly of inbred lines from the accessions collected in WCA.. - 1 Genome-wide distributions of 54,770 high quality single-nucleotide polymorphism (SNPs) derived from GBS of 309 pearl millet inbred lines.. - Table 1 Transition and transversion mutations of GBS-SNPs detected among 309 pearl millet genotypes. - subgroups found in the population structure analysis (Fig. - Sub- group 3 was formed with inbred lines derived from land- races/improved cultivars collected from various sources, and showed more dispersion than the other subgroups.. - Results showed that the subgroup 4 contained inbred lines derived from the source populations IP-3110, IP-6745, IP- 21142, PBPMPOP-1 and PBPMPOP-2, whereas group 5 comprised about 50% of inbred lines extracted from PBPMPOP-3.. - Most of the SNPs had a heterozygosity range of 0–25%. - Similarly, genetic purity of the lines in the population varied from 70 to 93%, with a mean of 85%. - Out of 309 inbred lines showed less than 10% heterozygosity had heterozygosity ranging from 11 to 20%, while 59 (about 20%) had het- erozygosity from 21 to 30%.. - Genetic differentiation of subgroups was calculated using F st -based analysis of the SNP data (Table 3). - The Fst coef- ficients showed that subgroup 2 could be considered as a subset of the whole panel used in this study with a very low Fst value as compared to the whole population (0.002). - Accessions from Group 5 showed lowest diversity in the population. - The average pairwise LD (r 2 ) across the gen- ome declined rapidly with increasing physical distance and most of the r 2 values were below 0.05 (Fig. - 7.2 kb), suggest- ing that a larger number of markers are required from chro- mosomes 1 and 4 than from chromosomes 3 and 7 for genome-wide association studies in pearl millet.. - In this study, 309 pearl millet inbred lines were geno- typed using GBS. - Using the pearl millet genome [37] as a reference and filtering the dataset resulted in the de- velopment of 54,770 high quality genome-wide SNPs.. - The level of heterozygosity of the SNPs ranged from of 0 to 20% with an average of 15%. - It has also been reported that high outcrossing rates, a sequencing error or mapping error may lead to high heterozygosity in pearl millet [19]. - The level of homozygosity of the genotypes ranged from 70 to 93%, with an average of 85%, which is ex- pected for inbred lines.. - The report revealed that the dis- tribution of the SNPs was dense in the telomeric regions. - than the pericentromeric regions of the pearl millet chromosomes probably because of low recombination rates, low gene density and/or low restriction sites for the enzymes around the centromere. - 4 Population structure of 309 pearl millet inbred lines. - The color of the vertical bar on the x-axis represents the proportion of membership of each inbred line in each subgroup. - low nucleotide diversity [15], and decreased natural and arti- ficial selection for alleles located in this part of the genome are both additional plausible reasons for lower marker numbers.. - As adaptive evolution is impli- cated in reducing functional diversity [18], genetic dis- tance among inbred lines derived from landraces grown in similar environments is expected to be low. - In the present study, population structure analysis using 30,893 SNPs detected five subgroups in a panel of 309 inbred lines and the grouping basically matches pedigree relationships or the parental source of the inbred lines. - Some genetic diversity studies reported six subpop- ulations in different panels of pearl millet [31, 32]. - Grouping of pearl millet inbred lines from the same geographic region into different subpopulations implies that selection for differ- ent traits is maintaining genetic diversity.. - A wide range of genotypic variations are prevalent in pearl millet for various agronomic traits and stress toler- ance as a result of its cultivation in diverse agro-climatic conditions and soil types [34]. - 5 The principal component analysis (a) and neighbor joining tree (b) of 309 pearl millet inbred lines. - productivity in pearl millet [28]. - Only a limited number of studies have assessed the evolutionary dynamics and genetic diversity patterns in pearl millet. - Genetic characterization of early- and late-flowering landraces from Senegal also indicated a large diversity in Senegal- ese pearl millet germplasm that may be useful in. - This study pro- vides a survey of genetic variation in pearl millet inbred lines from different geographic regions in Africa and Asia representing various agroecological niches. - How- ever, as the inbred lines were developed from landraces, improved varieties, and crosses between different geno- types, correlation of the subgroups to geographic origin could not be made.. - In pearl millet, genetic differentiation is important in the genetic im- provement of the crop for productivity and adaptation in the agriculturally marginal environments. - The genetic differentiation observed in the current study is the re- flection of the extent of genetic variation among the landraces and improved varieties grown in different areas. - 6 Single Nucleotide polymorphism (SNP) (a) and taxa heterozygosity (b) for 54,770 genome-wide SNPs markers detected among 309 pearl millet inbred lines. - Table 2 The nucleotide diversity ( π ) and Tajima ’ s D statistics among 309 pearl millet inbred lines grouped into five subpopulations. - pedigree is the reflection of geographic origin of the par- ents involved and selection history of the inbred lines, growing environment may had significant role in the for- mation of distinct forms that are distantly related. - A previous study conducted in Niger revealed also a moderate level of differenciation on cultivated pearl millet accessions compared to the wild populations [25]. - Screening 309 pearl millet lines with 54,770 high quality genome-wide SNPs re- vealed that genetic diversity is preserved in pearl millet inbred lines from Africa and the Indian subcontinent.. - diversity in subgroup 5, but high diversity in the other four subgroups. - A total of 309 inbred lines obtained from International Crop Research in Semi-Arid Tropics (ICRISAT-Niger) were used in this study (Additional file S1). - The inbred lines were developed following 4 to 6 generations of self- ing of landraces originating from WCA countries and Asia, and improved open pollinated varieties (OPV) with improved iron (Fe) and zinc (Zn) content.. - DNA extraction, library construction, and genotyping The seeds of the inbred lines were planted in a 96-cell trays in a greenhouse at Kansas State University. - The pearl millet reference genome (https://cegre- sources.icrisat.org/data_public/PearlMillet_Genome/v1.1 ) [37] was used to map GBS reads and identify SNPs using TASSEL 5.0 GBSv2 pipeline, (www.maizegenetics.. - The mapping of reads to the pearl millet refer- ence genome was done using BWA version 0.7.17-r1188 [23]. - Population structure of the SNP genotype datasets was analyzed using ADMIXTURE software [1] for K = 1 to 10. - To confirm the admixture results, PCA was performed using the snpgdsPCA function of the R package SNPRelate [41].. - SNP markers (54,770) developed for 309 pearl millet inbred lines.. - Relative kinship among pairs of inbred lines. - Genetic distance among pairs of inbred lines. - A western Sahara Centre of domestication inferred from pearl millet genomes. - Pearl millet hybrids. - proceedings of the international pearl millet workshop. - New genetic insights into pearl millet diversity as revealed by. - Population genomics of pearl millet (Pennisetum glaucum (L.) R. - Pearl millet minerals: effect of processing on bioaccessibility. - Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. - Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots. - Micronutrient density and stability in west African pearl millet — potential for biofortification. - Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits. - Genetic diversity, population structure, and linkage disequilibrium of pearl millet. - Genomic tools in pearl millet breeding for drought tolerance: status and prospects. - Exploration of genetic and genomic resources for abiotic and biotic stress tolerance in pearl millet. - Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt