Enhancing faba bean (Vicia faba L.) genome resources

Journal of Experimental Botany

Volumn 68, Issue 8, 2017, Pages 1941-1953

  Cooper, James W ^a   Wilson, Michael H ^a   Derks, Martijn F L ^b   Smit, Sandra ^b   Kunert, Karl J ^c   Cullis, Christopher ^d   Foyer, Christine H ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF PRETORIA   (South Africa)

^d CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Illumina sequencing; Legumes; Mitochondrial genome; Plastome; Protein security; RNA seq analysis

Indexed keywords

CROP; GENETICS; GENOMICS; MITOCHONDRIAL GENOME; PLANT BREEDING; PLANT GENOME; PROCEDURES; SEQUENCE ANALYSIS; VICIA FABA;

CROPS, AGRICULTURAL; GENOME, MITOCHONDRIAL; GENOME, PLANT; GENOMICS; PLANT BREEDING; SEQUENCE ANALYSIS, RNA; VICIA FABA;

EID: 85020270607     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erx117     Document Type: Article

References (60)

1. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Retrieved on 4 April 2017.
2. Arun-Chinnappa KS, McCurdy DW. 2015. De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research. Frontiers in Plant Science 6, 217.
3. Bao W, Kojima KK, Kohany O. 2015. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA 6, 11.
4. Barton L, Thamo T, Engelbrecht D, Biswas WK. 2014. Does growing grain legumes or applying lime cost effectively lower greenhouse gas emissions from wheat production in a semi-arid climate? Journal of Cleaner Production 83, 194-203.
5. Benedito VA, Torres-Jerez I, Murray JD, et al. 2008. A gene expression atlas of the model legume Medicago truncatula. The Plant Journal 55, 504-513.
6. Bennetzen JL. 2000. Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology 42, 251-269.
7. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2013. GenBank. Nucleic Acids Research 41, D36-D42.
8. Boye J, Zare F, Pletch A. 2010. Pulse proteins: processing, characterization, functional properties and applications in food and feed. Food Research International 43, 414-431.
9. Burstin J, Gallardo K, Mir RR, Varshney RK, Duc G. 2011. Improving protein content and nutrition quality. In: Pratap A, Kumar J, eds. Biology and breeding of food legumes. Wallingford, UK, CAB International, 314-328.
10. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10, 421.
11. Cernay C, Ben-Ari T, Pelzer E, Meynard JM, Makowski D. 2015. Estimating variability in grain legume yields across Europe and the Americas. Scientifc Reports 5, 11171.
12. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. 2012. Predicting the functional effect of amino acid substitutions and indels. PLoS One 7, e46688.
13. Csanad G, Pal M. 2014. Two distinct plastid genome confgurations and unprecedented intraspecies length variation in the accD coding region in Medicago truncatula. DNA Research 21, 417-427.
14. Davila JI, Arrieta-Montiel MP, Wamboldt Y, Cao J, Hagmann J, Shedge V, Xu YZ, Weigel D, Mackenzie SA. 2011. Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis. BMC Biology 9, 64.
15. Duc G, Moussy F, Zong X, Ding G. 1999. Single gene mutation for green cotyledons as a marker for the embryonic genotype in faba bean, Vicia faba. Plant Breeding 118, 577-578.
16. Duc G, Picard J. 1986. Note on the presence of the sym-1 gene in Vicia faba hampering its symbiosis with Rhizobium leguminosarum. Euphytica 35, 61-64.
17. Ellwood SR, Phan HT, Jordan M, Hane J, Torres AM, Avila CM, Cruz-Izquierdo S, Oliver RP. 2008. Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genomics 9, 380.
18. Erith AG. 1930. The inheritance of colour, size and form of seeds, and of fower colour in Vicia faba L. Genetica 12, 477-510.
19. FAOSTAT. 2016. United Nations Food and Agriculture Organisation Website. http://www.fao.org/faostat/en/. Retrieved on 4 April 2017.
20. Foyer CH, Lam HM, Nguyen HT, et al. 2016. Neglecting legumes has compromised human health and sustainable food production. Nature Plants 2, 16112.
21. Fuchs J, Strehl S, Brandes A, Schweizer D, Schubert I. 1998. Molecular-cytogenetic characterization of the Vicia faba genome-heterochromatin differentiation, replication patterns and sequence localization. Chromosome Research 6, 219-230.
22. Galtier N. 2011. The intriguing evolutionary dynamics of plant mitochondrial DNA. BMC Biology 9, 61.
23. Giordani T, Cossu RM, Mascagni F, Marroni F, Morgante M, Cavallini A, Natali L. 2016. Genome-wide analysis of LTR-retrotransposon expression in leaves of Populus × canadensis water-deprived plants. Tree Genetics and Genomes 12, 75.
24. Grandbastien MA. 2015. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. Biochimica et Biophysica Acta 1849, 403-416.
25. Griffths DW, Lawes DA. 1978. Variation in the crude protein content of feld beans (Vicia faba L.) in relation to the possible improvement of the protein content of the crop. Euphytica 27, 487-495.
26. Humann JL, Jung S, Zheng P, et al. 2016. Cool season food legume genome database: an up-to-date resource enabling genetics, genomics and breeding research in pea, lentil, faba bean and chickpea. Proceedings of the International Plant and Animal Genome Conference. San Diego, CA, USA.
27. Illumina. 2014. Sequencing methods review. A review of publications featuring Illumina Technology. Illumina Protocols 199, 27.
28. Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T, Paull J, Materne M, Forster JW. 2012. Transcriptome sequencing of feld pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13, 104.
29. Kelly LJ, Leitch IJ. 2011. Exploring giant plant genomes with next-generation sequencing characterization of the Vicia faba genome. Heterochromatin differentiation, replication patterns and sequence localization. Chromosome Research 6, 219-230.
30. Khazaei H, O'Sullivan DM, Sillanpää MJ, Stoddard FL. 2014. Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.). Theoretical and Applied Genetics 127, 2371-2385.
31. Kitazaki K, Kubo T, Kitazaki K, Kubo T. 2010. Cost of having the largest mitochondrial genome: evolutionary mechanism of plant mitochondrial genome. Journal of Botany 2010, 1-12.
32. Kode V, Mudd EA, Iamtham S, Day A. 2005. The tobacco plastid accD gene is essential and is required for leaf development. The Plant Journal 44, 237-244.
33. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-359.
34. Lassaletta L, Billen G, Grizzetti B, Anglade J, Garnier J. 2014. 50 year trends in nitrogen use effciency of world cropping systems: the relationship between yield and nitrogen input to cropland. Environmental Research Letters 9, 105011.
35. Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993.
36. Lisch D. 2002. Mutator transposons. Trends in Plant Science 7, 498-504.
37. Negruk V. 2013. Mitochondrial genome sequence of the legume Vicia faba. Frontiers in Plant Science 4, 128.
38. O'Rourke JA, Bolon YT, Bucciarelli B, Vance CP. 2014. Legume genomics: understanding biology through DNA and RNA sequencing. Annals of Botany 113, 1107-1120.
39. O'Sullivan DM, Angra D. 2016. Advances in Faba bean genetics and genomics. Frontiers in Genetics 7, 150.
40. Quinlan AR, Hall IM. 2010. BEDTools: a fexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
41. Ramsay G. 1997. Inheritance and linkage of a gene for testa-imposed seed dormancy in faba bean (Vicia faba L.). Plant Breeding 116, 287-289.
42. Ramundo S, Rahire M, Schaad O, Rochaix JD. 2013. Repression of essential chloroplast genes reveals new signaling pathways and regulatory feedback loops in Chlamydomonas. The Plant Cell 25, 167-186.
43. Ray H, Georges F. 2010. A genomic approach to nutritional, pharmacological and genetic issues of faba bean (Vicia faba): prospects for genetic modifcations. GM Crops 1, 99-106.
44. Rousseau-Gueutin M, Huang X, Higginson E, Ayliffe M, Day A, Timmis JN. 2013. Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages. Plant Physiology 161, 1918-1929.
45. Reichmann J, Crichton JH, Madej MJ, Taggart M, Gautier P, Garcia-Perez JL, Meehab RR, Adams IR. 2012. Microarray analysis of LTR retrotransposon silencing identifes Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PLoS Computational Biology 8, e1002486.
46. Roy F, Boye JI, Simpson BK. 2010. Bioactive proteins and peptides in pulse crops: pea, chickpea and lentil. Food Research International 43, 432-442.
47. Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen NA, Mutwakil M, Jansen R, Ruhlman T. 2014. Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnology Journal 12, 743-754.
48. Schnable PS, Ware D, Fulton RS, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112-1115.
49. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Research 19, 1117-1123.
50. Sjodin J. 1970. Induced asynaptic mutants in Vicia faba L. Hereditas 66, 215-232.
51. Sjodin J. 1971. Induced morphological variation in Vicia faba L. Hereditas 67, 155-180.
52. Temesgen T, Keneni G, Sefera T, Jarso M. 2015. Yield stability and relationships among stability parameters in faba bean (Vicia faba L.) genotypes. Crop Journal 3, 258-268.
53. Thorvaldsdóttir H, Robinson JT, Mesirov J P. 2013. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Briefngs in Bioinformatics 14, 178-192.
54. Torres AM, Avila CM, Gutierrez N, Palomino C, Moreno MT, Cubero JI. 2010. Marker-assisted selection in faba bean (Vicia faba L.). Field Crops Research 115, 243-252.
55. vaz Patto MC, Torres AM, Koblizkova A, Macas J, Cubero JI. 1999. Development of a genetic composite map of Vicia faba using F2 populations derived from trisomic plants. Theoretical and Applied Genetics 98, 736-743.
56. Webb A, Cottage A, Wood T, et al. 2016. A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). Plant Biotechnology Journal 14, 177-185.
57. Wicker T, Sabot F, Hua-Van A, et al. 2007. A unifed classifcation system for eukaryotic transposable elements. Nature Reviews. Genetics 8, 973-982.
58. Xu JH, Liu Q, Hu W, Wang T, Xue Q, Messing J. 2015. Dynamics of chloroplast genomes in green plants. Genomics 106, 221-231.
59. Yang T, Bao SY, Ford R, et al. 2012. High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 13, 602.
60. Zhang HM, Wheeler S, Xia X, Radchuk R, Weber H, Offer CE, Patrick JW. 2015. Differential transcriptional networks associated with key phases of ingrowth wall construction in trans-differentiating epidermal transfer cells of Vicia faba cotyledons. BMC Plant Biology 15, 103.