Investigation of the Relationship Between Genome Size and Some Agro morphological Characteristics in Common Bean (Phaseolus vulgaris L.) Accessions

Abstract

The common bean (Phaseolus vulgaris L.), one of the most well-known members of the legume family, is a very important source of protein, carbohydrates, vitamins, and minerals in the human diet. The objective of this study was to determine the correlation between genome size and some agro-morphological characteristics of 154 common bean accessions investigated in Tekirdağ condition. Based on the results of the flow cytometric analyses, it was determined that the mean genome sizes of the accessions varied between 1.28 pg2C-1 and 1.55 pg2C-1. When agromorphological characteristics were investigated, it was observed that plant height ranged from 28.8 to 327 cm, flowering time from 36.8 to 55.6 days, first pod formation from 44.6 to 63.8 days, first harvest time from 58.6 to 80.6 days, vegetation period from 81.4 to 100.2 days, number of pods per plant from 9.2 to 109 pods plant-1, number of seeds per pod from 1.66 to 7.34 seeds pod-1, 100-seed weight from 7.64 to 140.25 g, and seed yield per plant from 6.74 to 80.64 g plant-1. In the statistical analyses performance, it was found that the accessions had a wide variation in terms of all the characteristics studied (P<0.01). In addition, it was observed that dwarf beans flowered and formed pods earlier than climbing beans, but the number of seeds per plant, 100-seed weight, and seed yield per plant were higher in climbing beans compared to dwarf beans. Correlation analysis showed that there was a positive relationship between the genome sizes of accessions and some of their agro-morphological characteristics as flowering time, first pod formation, and vegetation period. In conclusion, the genetic resource collection of the common bean displayed significant variation for all characteristics investigated in the study and information on the genome size may provide alternative strategies to future breeding studies in selecting parents or genotypes with some specific agro-morphological characteristics.

Keywords

• Common bean (Phaseolus vulgaris L.)
• Flow cytometer
• Genome size
• Agro-morphology
• Variation
• Correlation

References

1. Asati B S & Singh A K (2008). Genetic components studies in French bean (Phaseolus vulgaris L.). New Agriculturist 19(1/2):117-123
2. Assefa T A, Mahama A, Brown A V, Cannon E K S, Rubyogo J C, Rao I M, Blair M W & Cannon S B (2019). A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.). Moleculer Breeding 39: 20. doi: 10.1007/s11032-018-0920-0
3. Ayonoadu U W U (1974). Nuclear DNA variation in Phaseolus. Chromosoma 48 (1): 41-49
4. Baetcke K, Sparrow A, Nauman C & Schwemmer S S (1967). The relationship of DNA content to nuclear and chromosome volumes and to radiosensitivity (LD50). Proceedings of the National Academy of Sciences 58:533-540. doi: 10.1073/pnas.58.2.533
5. Barow M & Meister A (2002). Lack of correlation between AT frequency and genome size in higher plants and the effect of nonrandomness of base sequences on dye binding. Cytometry 47 (1): 1–7. doi: 10.1002/cyto.10030
6. Basavaraja T, Manjunatha L, Chandora R, Gurumurthy S & Singh N P (2021). Assessment of genetic variability, diversity and trait correlation analysis in common bean (Phaseolus vulgaris L.) genotypes. Legume Research- An International Journal 44(3): 252-260. doi: 10.18805/LR-4208
7. Basavaraja T, Tripathi N, Chandora R, Pratap A, Manjuanatha L, Gurumurthy S, Singh M, Rana J C, Nitesh Kumar S D & Katiyar P K (2023). Evaluation of phenological development and agronomic traits in exotic common bean germplasm across multiple environments. Plant Genetic Resources 21(3):195-203. doi: 10.1017/S1479262123000618
8. Beaulieu J M, Leitch I J, Patel S, Pendharkar A & Knight C A (2008). Genome size is a strong predictor of cell size and stomatal density in angiosperms. New Phytologist 179(4): 975–986. doi: 10.1111/j.1469-8137.2008.02528.x

9. Beaulieu J M, Moles A T, Leitch I J, Bennett M D, Dickie J B & Knight C A (2007). Correlated evolution of genome size and seed mass. New Phytologist 173: 422-437. doi: 10.1111/j.1469-8137.2006.01919.x PMID: 17204088
10. Beletti P, Marzachi C & Lanteri S (1997). Flow cytometric estimation of nuclear DNA content in different species of Phaseolus. DI.VA.P.R.A. - Plant Breeding and Seed Production. Torino, Italy: University of Turin.
11. Bennett M D, Heslop-Harrison J S, Smith J B & Ward J P (1983). DNA density in mitotic and meiotic metaphase chromosomes of plants and animals. Journal of Cell Science 63:173–179. doi: 10.1242/jcs.63.1.173
12. Bennett M D & Leitch I J (1995). Nuclear DNA amounts in angiosperm. Annals of Botany 76 (2): 113-176. doi: 10.1006/anbo.1995.1085
13. Bennett M D & Leitch I J (2005). Plant DNA C-values Database (release 4.0, October 2005). http://data.kew.org/cvalues/
14. Bilinski P, Albert P S, Berg J J, Birchler J A, Grote M N, Lorant A, Quezada J, Swarts K, Yang J & Ross-Ibarra J (2018). Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. Plos Genetics 14(5): e1007162. doi: 10.1371/journal.pgen.1007162
15. Boros L, Wawer A & Borucka K (2014). Morphological, phenological and agronomical characterisation of variability among common bean (Phaseolus vulgaris L.). Local population from the national centre for plant genetic resources: Polish Genebank. Journal of Horticultural Research 22(2): 123-130. doi: 10.2478/johr-2014-0029
16. Bottini M C J, Greizerstein E J, Aulicino M B & Poggio L (2000). Relationships among genome size, environmental conditions and geographical distribution in natural populations of NW Patagonian species of Berberis L. (Berberidaceae). Annals of Botany 86 (3): 565573. doi: 10.1006/anbo.2000.1218
17. Burucu D (2023). Product report legume – 2023, Agricultural Economics and Policy Development Institute (TEPGE), Publication no: 391 (In Turkish).
18. Caproni L, Raggi L, Ceccarelli S, Negri V & Carboni A (2019). In-depth characterisation of common bean diversity discloses ıts breeding potential for sustainable agriculture. Sustainability 11(19): 5443. doi: 10.3390/su11195443
19. Castagnaro A P, Poggio L & Naranjo C A (1990). Nuclear DNA content variation in Phaseolus (Fabaceae). Darwiniana 30 (1/4): 195-200.
20. Chen Z, Guan Y, Han M, Guo Y, Zhang J, Guo Z, Sun G & Yan X (2022). Altitudinal patterns in adaptive evolution of genome size and ıntergenome hybridization between three Elymus species from the Qinghai–Tibetan Plateau. Front. Ecology and Evolution 10:923967. doi: 10.3389/fevo.2022.923967
21. Choudhary N, Gupta M, Shafi S, Jan S, Mir A H, Singh B & Mir R R (2022). Molecular diversity and nutriment studies of common bean. Crop & Pasture Science 73: 249–262. doi: 10.1071/CP21347
22. Coelho R C, Faria M A, Rocha J, Reis A, Oliveira M B P P & Nunes E (2009). Assessing genetic variability in germplasm of Phaseolus vulgaris L., collected in Northern Portugal. Scientia Horticulturae 122 (2009): 333-338. doi: 10.1016/j.scienta.2009.05.035
23. Comertpay G (2019). Assessment of nuclear DNA contents variation and their relationship with flowering in corn genotypes. Turkish Journal of Field Crops 24(1):39-45. doi: 10.17557/tjfc.562640
24. Dolezel J & Bartos J (2005). Plant DNA flow cytometry and estimation of nuclear genome size. Annals of Botany 95 (1): 99-110. doi: 10.1093/aob/mci005
25. Edwards G A & Endrizzi J L (1975). Cell size nuclear size and DNA content relationships in Gossypium. Canadian Journal of Genetics and Cytology 17:181–186. doi: 10.1139/g75-024
26. Elkoca E, Kantar F, Haliloğlu K, Adak A, Eken C & Dönmez M F (2022). Assessing genetic diversity by morphological markers of bean (Phaseolus vulgaris L.) germplasm from Northeast Anatolia. Atatürk University Journal of Agricultural Faculty 53(3):155-165. doi: 10.5152/AUAF.2022.98975
27. Evans G M, Rees H, Snell C L & Sun S (1972). The relation between nuclear DNA amount and the duration of the mitotic cycle. Chromosomes Today 3: 24–31
28. Fridley J D & Craddock A (2015). Contrasting growth phenology of native and invasive forest shrubs mediated by genome size. New Phytologist (2015) 207: 659–668. doi: 10.1111/nph.13384
29. Gregory T R, Hebert P D & Kolasa J (2000) Evolutionary implications of the relationship between genome size and body size in flatworms and copepods. Heredity 84: 201-208. doi: 10.1046/j.1365
30. IBPGR (1982). International Board for Plant Genetic Resources. Descriptors List for Phaseolus vulgaris, Secretariat Rome, Italy
31. Ikani V O, Falusi O A, Daudu O A Y & Abubakar A (2024). Agro-morphological characterization of Common bean accessions in northern region of Nigeria. Journal of Applied Biological Sciences 18(2): 209-222. doi: 10.5281/zenodo.12209644
32. Jakob S S, Meister A & Blattner F R (2004). The considerable genome size variation of Hordeum species (Poaceae) is linked to phylogeny, life form, ecology, and speciation rates. Molecular Biology and Evolution 21 (5): 860-869. doi: 10.1093/molbev/msh092
33. Jenkins G & Hasterok R (2007). BAC landing on chromosomes of Brachypodium distachyon for comparative genome alignment. Nature Protocols 2: 88-98. doi: 10.1038/nprot.2006.490
34. Jung C & Muller A E (2009). Flowering time control and applications in plant breeding. Trends in Plant Science 14(10):563–573. doi: 10.1016/j.tplants.2009.07.005
35. Kamfwa K, Cichy K A & Kelly J D (2015). Genome-wide association study of agronomic traits in common bean. The Plant Genome 8(2): 1 12. doi: 10.3835/bitki genomu2014.09.0059
36. Ketema W & Geleta N (2022). Studies on genetic variability of common bean (Phaseolus vulgaris l.) varieties for yield and yield related traits in western Ethiopia. International Journal of Applied Agricultural Sciences 8(1):41-49. doi: 10.11648/j.ijaas.20220801.15
37. Knight C A, Molinari N A & Petrov D A (2005). The Large Genome Constraint Hypothesis: Evolution, Ecology and Phenotype Annals of Botany 95: 177–190. doi: 10.1093/aob/mci011
38. Kouam E B, Kamga-Fotso A M & Anoumaa M (2023). Exploring agro-morphological profiles of Phaseolus vulgaris germplasm shows manifest diversity and opportunities for genetic improvement. Journal of Agriculture and Food Research 14:100772. doi: 10.1016/j.jafr.2023.100772
39. Kul R & Yıldırım E (2023). Evaluation of some agro-morphological characteristics of Dwarf Snap Bean genotypes collected from Erzurum province. Turkish Journal of Agriculture- Food Science and Technology, 11(6): 1087-1095. doi: 10.24925/turjaf.v11i6.1087-1095.5920
40. LabotanJ D, Miller T, Gil J, Ariza D, De la Hoz J F, Soler A, Beebe S, Duitama J, Gepts P & Raatz B (2018). Resequencing of common bean identifies regions of inter-gene pool introgression and provides comprehensive resources for molecular breeding. Plant Genome 11(2): 1 21. doi: 10.3835/ plantgenome2017.08.0068
41. Loko L E Y, Orobiyi A, Adjatin A, Akpo J, Toffa J, Djedatin G & Dansi A (2018). Morphological characterization of common bean (Phaseolus vulgaris L.) landraces of Central region of Benin Republic. Journal of Plant Breeding and Crop Sciences 10(11):304–318. doi: 10.5897/JPBCS2018.0766 Mekki L, Badr A & Fekry M (2007). Cytogenetic studies on nine genotypes of Phaseolus vulgaris L. cultivated in Egypt in relation to zinc efficiency. Pakistan Journal of Biological Sciences 10 (23): 4230-4235. doi: 10.3923/pjbs.2007.4230.4235
42. Nadeem M A, Karaköy T, Yeken M Z, Habyarimana E, Hatipoglu R, Çiftçi V, Nawaz M A, Sönmez F, Shahid M Q, Yang S H, Chung G & Baloch F S (2020). Phenotypic characterization of 183 Turkish common bean accessions for agronomic, trading, and consumer-preferred plant characteristics for breeding purposes. Agronomy 10 (2): 272- 282. doi: 10.3390/agronomy10020272
43. Nagl W & Treviranus A (1995). A flow cytometric analysis of the nuclear 2C DNA content in 17 Phaseolus species (53 genotypes). Botanica Acta 108 (5): 403-406. doi: 10.1111/j.1438-8677.1995.tb00513.x
44. Nemli S, Aşçıoğul T K, Ateş D, Eşiyok D & Tanyolaç M B (2017). Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkiye. Turkish Journal of Agriculture and Forestry 41 (5): 389-404. doi: 10.3906/tar- 1707-89
45. Ohri D (1998). Genome size variation and plant systematics. Annals of Botany 82 (1): 75-83. doi: 10.1006/anbo.1998.0765
46. Özkan H, Tuna M & Arumuganathan K (2003). Non-Additive Chandes in genome size during allopolyl, ploidization in the wheat (AegilopsTriticum) group. Journal of Heredity 94 (3),260-264. doi: 10.1093/jhered/esg053
47. Pandey V, Singh V K & Upadhyay D K (2013). Determination of green pod yield components in French bean (Phaseolus vulgaris L.) through correlation and path coefficient analyses. Vegetos 26(2):438-443. doi: 10.5958/J.2229-4473.26.2.108
48. Pedrosa-Harrand A, Souza de Almeida C C, Mosiolek M, Blair M W, Schweizer D & Guerra M (2006). Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theoretical and Applied Genetic 112 (5): 924-933. doi: 10.1007/s00122-005-0196-8
49. Pekşen E & Gülümser A (2005). Relationships and path analysis between yield and yield components in some bean (Phaseolus vulgaris L.) genotypes. Ondokuz Mayıs University Journal of Agriculture Faculty 20(3):82-87. doi: 10.7161/anajas.2005.20.3.82-87 (In Turkish) Porch T G, Beaver J S, Debouck D G, Jackson S A, Kelly J D & Dempewolf H (2013). Use of wild relatives and closely related species to adapt common bean to climate change. Agronomy 3 (2):433–461. doi: 10.3390/agronomy3020433
50. Rana J C, Sharma T R, Tyagi R K, Chahota R K, Gautam N K, Singh M, Sharma P N & Ojha S N et al. (2015). Characterisation of 4274 accessions of common bean (Phaseolus vulgaris L.) germplasm conserved in the Indian gene bank for phenological, morphological and agricultural traits. Euphytica 205:441–457. doi: 10.1007/s10681-015-1406-3
51. Rayburn A L, Dudley J W & Biradar D P (1994). Selection for early flowering results in simultaneous selection for reduced nuclear DNA content in maize. Plant Breeding 112 (4): 318–322. doi: 10.1111/j.1439-0523.1994.tb00690.x
52. Savaş Tuna G, Yücel G, Kaygısız Aşçıoğul T, Ateş D, Eşiyok D, Tanyolaç M B & Tuna M. 2020. Molecular cytogenetic characterization of common bean (Phaseolus vulgaris L.) accessions. Turkish Journal of Agriculture and Forestry 44: 612-630. doi: 10.3906/tar-1910-33
53. Scully B T & Wallace D H (1990). Variation in and relationship of biomass, growth rate, harvest ındex, and phenology to yield of common bean. American Society for Horticultural Science 115(2):218-225. doi: 10.21273/JASHS.115.2.218
54. Smarda P & Bures P (2006). Intraspecific DNA content variability in Festuca pallens on different geographical scales and ploidy levels. Annals of Botany 98 (1): 665-678. doi: 10.1093/aob/ mcl150
55. Souza G, Costa L, Guignard M S, Van-Lume B, Pellicer J, Gagnon E, Leitch I J & Lewis G P (2019). Do tropical plants have smaller genomes? Correlation between genome size and climatic variables in the Caesalpinia Group (Caesalpinioideae, Leguminosae). Perspectives in Plant Ecology, Evolution and Systematics 38:13-23. doi: 10.1016/j.ppees.2019.03.002
56. Stoilova T, Pereira G, Tavares de Sousa M M & Carnide V (2005). Diversity in common bean landraces (Phaseolus vulgaris L.) from Bulgaria and Portugal. Journal of Central European Agriculture 6 (4), 443-448.
57. Tenaillon M I, Manicacci D, Nicolas S D, Tardieu F & Welcker C (2016). Testing the link between genome size and growth rate in maize. Peer Journal 4:e2408. doi: 10.7717/peerj.2408. eCollection 2016
58. Tomlekova N, Idziak-Helmcke D, Franke P, Rojek-Jelonek M & Kwasniewska J (2024). Phaseolus vulgaris mutants reveal variation in the nuclear genome. Frontiers in Plant Science 14:1308830. doi: 10.3389/fpls.2023.1308830
59. Vesely P, Bures P, Smarda P & Pavlıcek T (2012). Genome size and DNA base composition of geophytes: the mirror of phenology and ecology. Annals of Botany 109: 65–75. doi: 10.1093/aob/mcr267
60. Wang B, Mao J F, Zhao W & Wang X R (2013). Impact of geography and climate on the genetic differentiation of the subtropical pine Pinus yunnanensis. PLoS ONE 8 (6): e67345. doi: 10.1371/journal.pone.0067345
61. Zhang F P & Zhang S B (2021). Genome size and labellum epidermal cell size are evolutionarily correlated with floral longevity in Paphiopedilum species. Frontiers in Plant Science 12:793516. doi: 10.3389/fpls.2021.793516