Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data

Fu, Yong‐Bi

doi:10.3390/plants12071476

Cited by 3 publications

(5 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…. The significant association between the total mutation burden estimates generated in this study and the average pairwise difference estimates acquired from the previous study [29].…”

Section: Correlating Between Mutation Burdens and Averaged Pairwise D...supporting

confidence: 55%

“… The significant association between the total mutation burden estimates generated in this study and the average pairwise difference estimates acquired from the previous study [ 29 ]. The selection target zone (in the rectangle) for germplasm with higher average pairwise difference estimates and lower total mutation burden estimates is also illustrated.…”

Section: Figurementioning

confidence: 60%

“…A correlation analysis between sample-wise total mutation burdens and sample-wise averaged pairwise differences (APDs) that were estimated from the same published SNP data [ 29 ] revealed a significantly positive correlation between the two estimations ( Figure 5 ). This result is novel and interesting, as a sample with a higher mutation burden estimate had a higher average pairwise genetic difference estimate.…”

Section: Resultsmentioning

confidence: 99%

“…Fourth, a correlation was also made between the estimates of total mutation burdens and APDs of individual samples. The APD data (or Hordeum-vulgare-passport-APD.xlsx) was previously generated from the analysis of genetic distinctness and redundancy for 19,778 barley samples based on the same SNP genotype data set [ 29 ]. The larger the APD value, the more genetically distinct the sample is from the other samples, allowing for the measurement of sample genetic distinctness or redundancy [ 47 ].…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ

2024

IJMS

Self Cite

View full text Add to dashboard Cite

Long-term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide is a challenging mission. The extent of deleterious mutations present in conserved germplasm and the genetic risk associated with accumulative mutations are largely unknown. This study took advantage of published barley genomic data to predict sample-wise mutation burdens for 19,778 domesticated barley (Hordeum vulgare L.) accessions conserved ex situ. It was found that the conserved germplasm harbored 407 deleterious mutations and 337 (or 82%) identified deleterious alleles were present in 20 (or 0.1%) or fewer barley accessions. Analysis of the predicted mutation burdens revealed significant differences in mutation burden for several groups of barley germplasm (landrace > cultivar (or higher burden estimate in landrace than in cultivar); winter barley > spring barley; six-rowed barley > two-rowed barley; and 1000-accession core collection > non-core germplasm). Significant differences in burden estimate were also found among seven major geographical regions. The sample-wise predicted mutation burdens were positively correlated with the estimates of sample average pairwise genetic difference. These findings are significant for barley germplasm management and utilization and for a better understanding of the genetic risk in conserved plant germplasm.

show abstract

“…. The significant association between the total mutation burden estimates generated in this study and the average pairwise difference estimates acquired from the previous study [29].…”

Section: Correlating Between Mutation Burdens and Averaged Pairwise D...supporting

confidence: 55%

Section: Figurementioning

confidence: 60%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ

2024

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…In recent years, the advent of high-throughput sequencing technologies has revolutionized the characterization of genebank crop collections, such as wheat, barley, bean, cassava, and rice ( Nadeem et al., 2018 ; Ferguson et al., 2019 ; Milner et al., 2019 ; Sansaloni et al., 2020 ; Tanaka et al., 2021 ). These techniques examine genome-wide natural variation patterns ( Orek et al., 2023 ) and enable the comprehensive assessment of genetic distinctness and redundancy across entire genomes ( Fu, 2023 ; Orek et al., 2023 ). The genetic distinctness and redundancy of cassava clones grown by farmers or conserved in genebanks has been evaluated using a variety of methods, revealing genetic redundancy levels of 20−50 percent within and across collections ( Chavarriaga-Aguirre et al., 1999 ; Albuquerque et al., 2019 ; Orek et al., 2023 ; Soro et al., 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Identifying genetically redundant accessions in the world’s largest cassava collection

Carvajal-Yepes,

Ospina,

Aranzales

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava (Manihot esculenta) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT’s cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions.

show abstract

Genetically Distinct Rice Lines for Specific Characters as Revealed by Gene-Associated Average Pairwise Dissimilarity

2024

Crops

View full text Add to dashboard Cite

Broadening the genetic base of an elite breeding gene pool is one important goal in a successful long-term plant breeding program. This goal is largely achieved through the search for and introgression of exotic germplasm with adaptive traits. However, little is known about the genetic backgrounds of acquired exotic germplasm, as germplasm selection is mainly based on trait information. Here, we expanded an average pairwise dissimilarity (APD) analysis to samples with SNP genotypes associated with genes for specific characters of breeding interest. Specifically, we explored a gene-associated APD analysis in a genomic characterization of 2643 rice lines based on their published FASTQ data. Published contigs for cloned genes conditioning heat tolerance, cold tolerance, fertility, and seed size were downloaded as gene reference sequences for SNP calling, along with those SNP calls based on the rice reference genome and published indels. Totally, eight SNP or indel data sets were formed for each of three sample groups (All2643, Indica1789, and Japonica854). APD estimation was made for each of the 24 data sets. For each sample group, four novel sets of the 25 most genetically distinct rice lines, each for an assayed character, were identified. Further analyses of APD estimates also revealed some interesting APD properties. Four contig-based SNP data sets for four specific characters displayed similar APD frequency distributions and positive high correlations of APD estimates. Contig-based APD estimates were negatively correlated with genome-based APD estimates and nearly uncorrelated with indel-based APD estimates. These findings are significant for plant germplasm characterization and germplasm utilization in plant breeding.

show abstract

Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data

Cited by 3 publications

References 38 publications

Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ

Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ

Identifying genetically redundant accessions in the world’s largest cassava collection

Genetically Distinct Rice Lines for Specific Characters as Revealed by Gene-Associated Average Pairwise Dissimilarity

Contact Info

Product

Resources

About