SNP Markers and its Impact on Crop Improvement

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159–MR167) to 0.723 (MRIA–Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

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Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽

10.1371/journal.pone.0243238 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243238

Author(s):

Wilson Nkhata ◽

Hussein Shimelis ◽

Rob Melis ◽

Rowland Chirwa ◽

Tenyson Mzengeza ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Common Bean ◽

Southern Africa ◽

Crop Improvement ◽

Phenotypic Expression ◽

Snp Markers ◽

High Yield ◽

Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401479 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3651-3661 ◽

Cited By ~ 1

Author(s):

Moses Nyine ◽

Elina Adhikari ◽

Marshall Clinesmith ◽

Katherine W. Jordan ◽

Allan K. Fritz ◽

...

Keyword(s):

Crop Improvement ◽

Aegilops Tauschii ◽

Allelic Diversity ◽

Sequence Divergence ◽

Snp Markers ◽

D Genome ◽

Entire Genome ◽

Wild Allele ◽

The Hill ◽

Genomic Patterns

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.

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Genetic Structure of Wild Germplasm of Macadamia: Species Assignment, Diversity and Phylogeographic Relationships

Plants ◽

10.3390/plants9060714 ◽

2020 ◽

Vol 9 (6) ◽

pp. 714 ◽

Cited By ~ 2

Author(s):

Thuy Mai ◽

Mobashwer Alam ◽

Craig Hardner ◽

Robert Henry ◽

Bruce Topp

Keyword(s):

Genetic Structure ◽

Crop Improvement ◽

Geographic Distance ◽

Mantel Test ◽

Snp Markers ◽

Principal Coordinate Analysis ◽

Conservation Strategy ◽

Wild Germplasm ◽

Test Analysis ◽

Macadamia Integrifolia

Macadamia is an Australian native rainforest tree that has been domesticated and traded internationally for its premium nuts. Common cultivars rely upon a limited gene pool that has exploited only two of the four species. Introducing a more diverse germplasm will broaden the genetic base for future crop improvement and better adaptation for changing environments. This study investigated the genetic structure of 302 accessions of wild germplasm using 2872 SNP and 8415 silicoDArT markers. Structure analysis and principal coordinate analysis (PCoA) assigned the 302 accessions into four distinct groups: (i) Macadamia integrifolia, (ii) M. tetraphylla, and (iii) M. jansenii and M. ternifolia, and (iv) admixtures or hybrids. Assignment of the four species matched well with previous characterisations, except for one M. integrifolia and four M. tetraphylla accessions. Using SNP markers, 94 previously unidentified accessions were assigned into the four distinct groups. Finally, 287 accessions were identified as pure examples of one of the four species and 15 as hybrids of M. integrifolia and M. tetraphylla. The admixed accessions showed the highest genetic diversity followed by M. integrifolia, while M. ternifolia and M. jansenii accessions were the least diverse. Mantel test analysis showed a significant correlation between genetic and geographic distance for M. integrifolia (r = 0.51, p = 0.05) and a positive but not significant correlation for M. tetraphylla (r = 0.45, p = 0.06). This study provides a population genetics overview of macadamia germplasm as a background for a conservation strategy and provides directions for future macadamia breeding.

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Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

Scientific Reports ◽

10.1038/s41598-021-87284-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jeewan Pandey ◽

Douglas C. Scheuring ◽

Jeffrey W. Koym ◽

Joseph Coombs ◽

Richard G. Novy ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Skin Color ◽

Potato Breeding ◽

Crop Improvement ◽

Snp Markers ◽

Breeding Program ◽

Potato Breeding Program ◽

The Usa

AbstractKnowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.

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KASPar SNP genetic map of cassava for QTL discovery of productivity traits in moderate drought stress environment in Africa

Scientific Reports ◽

10.1038/s41598-021-90131-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Favour Ewa ◽

Joseph N. A. Asiwe ◽

Emmanuel Okogbenin ◽

Alex C. Ogbonna ◽

Chiedozie Egesi

Keyword(s):

Crop Improvement ◽

Molecular Genetic ◽

Complex Trait ◽

Interval Mapping ◽

Growth Cycle ◽

Molecular Genetic Analysis ◽

Snp Markers ◽

Genetic Dissection ◽

Molecular Tools ◽

High Performing

AbstractCassava is an important staple in Sub-Sahara Africa. While its production has rapidly expanded to the dry savannahs of the continent, productivity is low in this ecology due to drought by farmers, extending the growth cycle from 12 months to 18, and sometimes 24 months to ensure better harvests. Yield is a complex trait and often difficult to manipulate for genetic gain in conventional breeding. Unfortunately, the dearth of molecular tools for decades has hampered molecular breeding (MB) to improve cassava productivity. This study was conducted to explore KASpar SNPs to generate more molecular tools to enhance genetic dissection of elite African germplasm for improved cassava productivity in dry environments of Africa where molecular resources are highly limited for crop improvement. To aid molecular genetic analysis of traits, a linkage map covering 1582.8 cM with an average resolution of 3.69 cM was constructed using 505 polymorphic SNP markers distributed over 21 linkage groups. Composite interval mapping using 267 F1 progeny in initial QTL mapping identified 27 QTLs for productivity traits in the dry savannah of Nigeria. The availability of KASPar SNPs are anticipated to improve the implementation of MB for the development of high performing drought-tolerant cassava varieties in Africa.

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Identification of Early Tomato Fruit Ripening Loci by QTL-seq

Journal of Agricultural Science ◽

10.5539/jas.v11n2p51 ◽

2019 ◽

Vol 11 (2) ◽

pp. 51

Author(s):

E. Ruangrak ◽

Yongchen Du ◽

Nang Myint Phyu Sin Htwe ◽

Pimpan Pimorat ◽

Jianchang Gao

Keyword(s):

Candidate Genes ◽

Fruit Ripening ◽

Tomato Fruit ◽

Crop Improvement ◽

Snp Markers ◽

Glycoside Hydrolases ◽

Fruit Softening ◽

Chromosome 11 ◽

Tomato Fruit Ripening ◽

Early Ripening

QTL-seq has been successfully studied in identifying major QTLs, markers, and candidate genes associated with traits that are important for crop improvement. Tomato earliness is an economically important trait and is a major current research focus recently. This paper reports the identification of tomato early ripening fruit locus facilitated by QTL-seq using a novel next-generation sequencing technology. Two DNA pools of phenotypes of F2 offspring from crosses between the Bone ММ (early ripening fruit, P1) and 071-440 (late ripening fruit, P2) cultivars of (Solanum lycopersicum) were bulked for sequencing and alignment analysis. Sequencing results revealed 434 SNP markers on chromosome 11, a candidate QTL at position 52,048,208 bp (named er-fruit) and a candidate gene, Solyc11g071510.1.1. The “er-fruit” as confirmed by the traditional QTL method was related to the early fruit ripening trait in tomato. Additionally, BLAST analysis to known homologies for Solyc11g071510.1.1 gene encodes glycoside hydrolases (GHs). GHs are functionally associated with cell wall degradation, fruit softening and ripening. Thus, GHs may be important in fruit softening, stimulating early fruit ripening in tomato. Our results confirmed that QTL-seq is effective method to identify candidate QTL loci, candidate genes and candidate markers.

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Genetic Diversity Assessment of Four Rice Varieties using SNP Markers

European Journal of Engineering Research and Science ◽

10.24018/ejers.2017.2.12.504 ◽

2017 ◽

Vol 2 (12) ◽

pp. 17 ◽

Cited By ~ 1

Author(s):

Oumarou Souleymane ◽

Batieno Teyioué Benoit Joseph ◽

Baboucarr Manneh ◽

Kwadwo Ofori ◽

Eric Danquah

Keyword(s):

Salt Tolerance ◽

Crop Improvement ◽

Dry Weight ◽

Snp Markers ◽

Phenotypic Traits ◽

Substitution Pattern ◽

Rice Varieties ◽

Phenotypic Data ◽

Panicle Number ◽

Diversity Assessment

Markers assisted selection is a tool for improving the speed and efficiency of crop improvement. The identification of SNPs within the target genomic region of a QTL is necessary for efficient breeding of quantitative traits such as salt tolerance. The study was conducted to characterize parental lines using SNP markers and to identify the polymorphic SNPs for salt tolerance in QTL study of offspring. Four rice lines were evaluated under five levels of salt conditions including the control. The experimental design was a split-plot with two replications. Leaf samples were collected from four rice lines at heading stage and sent to LGC Genomics laboratory for genotyping using rice SNP platform. DNA extraction and SNP genotyping were performed using an internal protocol. The phenotypic data recorded were the visual scoring, tiller number, green leaf number, panicle number, panicle weight and dry weight. Phenotypic data were analyzed using SAS 9.2 software. The genotypic data were analyzed using MEGA6 and GGT2 software. Significant diversity was revealed among lines concerning all the phenotypic traits. Significant diversity, divergence and substitution pattern were observed among lines. 200 markers out of 1896 were polymorphic and selected for the next step.

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High-resolution genetic map construction and QTL analysis of important fiber traits in kenaf using RAD-seq

10.21203/rs.3.rs-1072676/v1 ◽

2021 ◽

Author(s):

Li Hui ◽

Chang Li ◽

Tang Huijuan ◽

Luan Mingbao ◽

Pan Gen ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

Fiber Quality ◽

Crop Improvement ◽

Molecular Genetic ◽

Snp Markers ◽

Linkage Groups ◽

Genetic Traits ◽

Map Construction ◽

Fiber Yield

Abstract Quantitative trait locus (QTL) mapping is a useful method for revealing the mechanism of complex genetic traits and identifying new genomic information to accelerate crop improvement. In the present study, 154 F2:3 strains and their parents were used for restriction site-associated DNA sequencing, single-nucleotide polymorphism (SNP) identification, and genetic map construction. After filtering based on stringent filtering standards, 297.5 Gb of clean data were obtained. Further, 5,191 polymorphic SNP markers were identified from each sample, of which 1,997 polymorphic SNP markers were successfully mapped onto 18 different linkage groups. Six QTLs (QPH, QFBW, QDBW, QFW, QFT, and QFC) were identified based on the genetic map using the multiple QTL mapping (MQM) method, which were then assigned to three linkage groups, LG16, LG8, and LG3. QPH, QFBW, QDBW, and QFW were related to fiber yield, while QFT and QFC were related to fiber quality. This is the first study of its kind to map QTL of fiber yield and fiber quality, which will facilitate further understanding of the molecular genetic basis of these traits. However, there are limitations regarding the utilization of this map because several large gaps remain in some linkage groups. Therefore, additional markers need to be developed to further narrow these regions.

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Linkage disequilibrium and population structure in a core collection of Brassica napus (L.)

10.1101/2021.04.06.438572 ◽

2021 ◽

Author(s):

Mukhlesur Rahman ◽

Ahasanul Hoque ◽

Jayanta Roy

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Core Collection ◽

Crop Improvement ◽

Snp Markers ◽

Hybrid Breeding ◽

Brassica Napus L ◽

A Genome ◽

C Genome

AbstractEstimation of genetic diversity in rapeseed/canola is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed/canola germplasm using 8,502 single nucleotide polymorphism (SNP) markers. The germplasm accessions were divided into five subpopulations (P1 to P5) with obvious geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb), relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. To maximize genetic gain, hybridization between rutabaga and other types are potentially the best option. Hybridization between spring and winter, semi-winter type is also helpful to maximize the diversity in subsequent populations. Low genetic differentiation between both spring type subpopulations (P4 and P3) will accelerate favorable allele accumulation for specific traits in elite lines. The Neighbor-Joining tree and kinship matrix will assist to identify distantly related genotypes from subpopulations to utilize in hybridization. The low levels of LD and population structure make the core collection an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.

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