Role of Genomics in Promoting the Utilization of Plant Genetic Resources in Genebanks

Overview

Journal Brief Funct Genomics

Publisher Oxford University Press

Date 2018 Apr 25

PMID 29688255

Citations 29

Authors

Peterson W Wambugu

Marie-Noelle Ndjiondjop

Robert J Henry

Affiliations

Soon will be listed here.

Abstract

Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended.

Citing Articles

Optimizing the accession-level quantity of seeds to put into storage to minimize seed (gene)bank regeneration or re-collection.

Hay F, Baum Nee Whitehouse K, Oyatomi O, Wolkis D Conserv Physiol. 2025; 13(1):coaf011.

PMID: 39996017 PMC: 11849998. DOI: 10.1093/conphys/coaf011.

High-quality phenotypic and genotypic dataset of barley genebank core collection to unlock untapped genetic diversity.

Yuan Z, Rembe M, Mascher M, Stein N, Himmelbach A, Jayakodi M Gigascience. 2025; 14.

PMID: 39931028 PMC: 11811526. DOI: 10.1093/gigascience/giae121.

Genotyping Genebank Collections: Strategic Approaches and Considerations for Optimal Collection Management.

Anglin N, Wenzl P, Azevedo V, Lusty C, Ellis D, Gao D Plants (Basel). 2025; 14(2).

PMID: 39861604 PMC: 11768347. DOI: 10.3390/plants14020252.

Agricultural landscape genomics to increase crop resilience.

Campbell Q, Bedford J, Yu Y, Halpin-McCormick A, McCormick A, Castaneda-Alvarez N Plant Commun. 2025; 6(2):101260.

PMID: 39849843 PMC: 11897451. DOI: 10.1016/j.xplc.2025.101260.

Research and developmental strategies to hasten the improvement of orphan crops.

Akpojotor U, Oluwole O, Oyatomi O, Paliwal R, Abberton M GM Crops Food. 2024; 16(1):46-71.

PMID: 39718143 PMC: 11702946. DOI: 10.1080/21645698.2024.2423987.

References

McCouch S, Baute G, Bradeen J, Bramel P, Bretting P, Buckler E . Agriculture: Feeding the future. Nature. 2013; 499(7456):23-4. DOI: 10.1038/499023a. View

Brozynska M, Omar E, Furtado A, Crayn D, Simon B, Ishikawa R . Chloroplast Genome of Novel Rice Germplasm Identified in Northern Australia. Trop Plant Biol. 2014; 7(3-4):111-120. PMC: 4245483. DOI: 10.1007/s12042-014-9142-8. View

Li S, Xie K, Li W, Zou T, Ren Y, Wang S . Re-sequencing and genetic variation identification of a rice line with ideal plant architecture. Rice (N Y). 2016; 5(1):18. PMC: 5520836. DOI: 10.1186/1939-8433-5-18. View

Flint-Garcia S, Thornsberry J, Buckler 4th E . Structure of linkage disequilibrium in plants. Annu Rev Plant Biol. 2003; 54:357-74. DOI: 10.1146/annurev.arplant.54.031902.134907. View

Xu X, Liu X, Ge S, Jensen J, Hu F, Li X . Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol. 2011; 30(1):105-11. DOI: 10.1038/nbt.2050. View

Han Y, Lv P, Hou S, Li S, Ji G, Ma X . Combining Next Generation Sequencing with Bulked Segregant Analysis to Fine Map a Stem Moisture Locus in Sorghum (Sorghum bicolor L. Moench). PLoS One. 2015; 10(5):e0127065. PMC: 4436200. DOI: 10.1371/journal.pone.0127065. View

Wambugu P, Brozynska M, Furtado A, Waters D, Henry R . Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep. 2015; 5:13957. PMC: 4564799. DOI: 10.1038/srep13957. View

Lewis T, Loman N, Bingle L, Jumaa P, Weinstock G, Mortiboy D . High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect. 2010; 75(1):37-41. DOI: 10.1016/j.jhin.2010.01.012. View

Yu J, Buckler E . Genetic association mapping and genome organization of maize. Curr Opin Biotechnol. 2006; 17(2):155-60. DOI: 10.1016/j.copbio.2006.02.003. View

10.

Hospital F . Size of donor chromosome segments around introgressed loci and reduction of linkage drag in marker-assisted backcross programs. Genetics. 2001; 158(3):1363-79. PMC: 1461714. DOI: 10.1093/genetics/158.3.1363. View

11.

Michelmore R, Paran I, Kesseli R . Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A. 1991; 88(21):9828-32. PMC: 52814. DOI: 10.1073/pnas.88.21.9828. View

12.

Studholme D . Application of high-throughput genome sequencing to intrapathovar variation in Pseudomonas syringae. Mol Plant Pathol. 2011; 12(8):829-38. PMC: 6640474. DOI: 10.1111/j.1364-3703.2011.00713.x. View

13.

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y . Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010; 42(11):961-7. DOI: 10.1038/ng.695. View

14.

Thudi M, Li Y, Jackson S, May G, Varshney R . Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics. 2012; 11(1):3-11. DOI: 10.1093/bfgp/elr045. View

15.

Singh V, Khan A, Saxena R, Kumar V, Kale S, Sinha P . Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnol J. 2015; 14(5):1183-94. PMC: 5054876. DOI: 10.1111/pbi.12470. View

16.

Harkins G, Martin D, Duffy S, Monjane A, Shepherd D, Windram O . Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. J Gen Virol. 2009; 90(Pt 12):3066-3074. PMC: 2885043. DOI: 10.1099/vir.0.015537-0. View

17.

Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q . Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet. 2011; 44(1):32-9. DOI: 10.1038/ng.1018. View

18.

Fukuoka S, Saka N, Koga H, Ono K, Shimizu T, Ebana K . Loss of function of a proline-containing protein confers durable disease resistance in rice. Science. 2009; 325(5943):998-1001. DOI: 10.1126/science.1175550. View

19.

McCoy R, Taylor R, Blauwkamp T, Kelley J, Kertesz M, Pushkarev D . Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One. 2014; 9(9):e106689. PMC: 4154752. DOI: 10.1371/journal.pone.0106689. View

20.

Lefeuvre P, Martin D, Harkins G, Lemey P, Gray A, Meredith S . The spread of tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathog. 2010; 6(10):e1001164. PMC: 2965765. DOI: 10.1371/journal.ppat.1001164. View