Genetic Diversity, Population Structure, and Linkage Disequilibrium of Pearl Millet

Serba, Desalegn D.; Muleta, Kebede T.; Amand, Paul St.; Bernardo, Amy; Bai, Guihua; Perumal, Ramasamy; Bashir, Elfadil

doi:10.3835/plantgenome2018.11.0091

Cited by 49 publications

(51 citation statements)

References 72 publications

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“…Although some progresses have been made in understanding of origin of Basmati genome, further study is needed to identify the Basmati-specific genome features and genome variation by assembling the traditional Basmati varieties compared with japonica, indica, and aus groups. Next-generation sequencing (NGS) technologies are important for genomic analysis and molecular breeding (Chen et al, 2014), and enable the identification of functional genomic variation, and unique SNPs, and insertion-deletion polymorphisms (InDels) across the genome, which offer an exciting opportunity to genetic diversity studies in the crop plants (Jimenez et al, 2013;Serba et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

et al. 2020

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Basmati is considered a unique varietal group of rice (Oryza sativa L.) because of its aroma and superior grain quality. Previous genetic analyses of rice showed that most of the Basmati varieties are classified into the aromatic group. Despite various efforts, genomic relationship of Basmati rice with other varietal groups and genomic variation in Basmati rice are yet to be understood. In the present study, we resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare (japonica rice), Kasalath (aus rice), and Zhenshan 97 (indica rice). Comparison of these sequences revealed common single nucleotide polymorphisms (SNPs) in the genic regions of three Basmati varieties. Analysis of these SNPs revealed that Basmati varieties showed fewer sequence variations compared with the aus group than with the japonica and indica groups. Gene ontology (GO) enrichment analysis indicated that SNPs were present in genes with various biological, molecular, and cellular functions. Additionally, functional annotation of the Basmati mutated gene cluster shared by Nipponbare, Kasalath, and Zhenshan 97 was found to be associated with the metabolic process involved in the cellular aromatic compound, suggesting that aroma is an important specific genomic feature of Basmati varieties. Furthermore, 30 traditional Basmati varieties were classified into three different groups, aromatic (22 varieties), aus (four varieties), and indica (four varieties), based on genome-wide SNPs. All 22 aromatic Basmati varieties harbored the fragrant-inducing Badh2 allele. We also performed comparative analysis of 13 key agronomic and grain quality traits of Basmati rice and other rice varieties. Three traits including length-to-width ratio of grain (L/W ratio), panicle length (PL), and amylose content (AC) showed significant (P < 0.05 and P < 0.01) differences between the aromatic and indica/aus groups. Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the aus and japonica groups. Overall, whole-genome sequence data and genetic diversity information obtained in this study will

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Section: Introductionmentioning

confidence: 99%

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

et al. 2020

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“…GWAS across 288 testcross progenies of PMiGAP was also conducted for 20 grain yield and stover yield component trait and identified 1054 strongly significant marker-trait association for 15 of the traits (Varshney et al 2017). A study of genomic diversity, population structure, and linkage disequilibrium conducted on 398 accessions from different geographic regions provided a noteworthy insight (Serba et al 2019). Data analysis using a total of 82,112 genome-wide SNPs discovered through GBS revealed hierarchical genetic structure of six subgroups that mostly overlap with the geographic origins (west Africa, east Africa, Southern Africa, the Middle East, India, and lines developed in USA).…”

Section: Potential Of Association Studies For Germplasm Enhancementmentioning

confidence: 99%

Genomic Designing of Pearl Millet: A Resilient Crop for Arid and Semi-arid Environments

Serba

Yadav

Varshney

et al. 2020

Genomic Designing of Climate-Smart Cereal Crops

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Pearl millet [Pennisetum glaucum (L.) R. Br.; Syn. Cenchrus americanus (L.) Morrone] is the sixth most important cereal in the world. Today, pearl millet is grown on more than 30 million ha mainly in West and Central Africa and the Indian sub-continent as a staple food for more than 90 million people in agriculturally marginal areas. It is rich in proteins and minerals and has numerous health benefits such as being gluten-free and having slow-digesting starch. It is grown as a forage crop in temperate areas. It is drought and heat tolerant, and a climate-smart crop that can withstand unpredictable variability in climate. However, research on pearl millet improvement is lagging behind other major cereals mainly due to limited investment in terms of man and money power. So far breeding achievements include the development of cytoplasmic male sterility (CMS), maintenance counterparts (rf) system and nuclear fertility restoration genes (Rf) for hybrid breeding, dwarfing genes for reduced height, improved input responsiveness, photoperiod neutrality for short growing season, and resistance to important diseases. Further improvement of pearl millet for genetic yield potential, stress tolerance, and nutritional quality traits would enhance food and nutrition security for people living in agriculturally dissolute environments. Application of molecular technology in the pearl millet breeding program has a promise in enhancing the selection efficiency while shortening the lengthy phenotypic selection process

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“…Fresh leaf tissues pooled from four to six seedlings per line were collected seven days after planting, and freeze-dried for 48 h to remove water rapidly. Genomic DNA was extracted following a modified 2% CTAB protocol as previously described (Serba et al, 2019 LD analysis was performed using TASSEL as a standardized disequilibrium coefficient (D') (Hedrick, 1987) and squared allele-frequency correlations (r 2 ) (Weir, 1996) among pairs of loci. LD decay was fitted using a nonlinear ls function in R. Genetic difference among the identified subgroups were determined using Fst across the SNPs as a measure of population differentiation due to genetic structure.…”

Section: Dna Extraction Library Construction and Genotypingmentioning

confidence: 99%

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

Serba

Kanfany

Rhodes

et al. 2020

Preprint

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Background: Genetic improvement of pearl millet is lagging behind most of the major crops.Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding.Results: Sequencing the genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. 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. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. 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. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping. BackgroundPearl millet (Pennisetum glaucum (L.) R. Br. syn. Cenchrus americanus (L.) Morrone) is a climateresilient crop grown in the arid and semi-arid areas of the world. Pearl millet is the most widely grown millet species, accounting for approximately half of the total worldwide production of millets (Taylor,

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Genetic Diversity, Population Structure, and Linkage Disequilibrium of Pearl Millet

Cited by 49 publications

References 72 publications

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

Genomic Designing of Pearl Millet: A Resilient Crop for Arid and Semi-arid Environments

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

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