Korean Journal of Plant Resources (한국자원식물학회지)

The Plant Resources Society of Korea (한국자원식물학회)
권호 표지
DOI QR코드

DOI QR Code

An Analysis of the Heritability of Phenotypic Traits Using Chloroplast Genomic Information of Legume Germplasms

엽록체 유전정보를 이용한 두류 유전자원 형태적 형질의 유전력 분석

  • Dong Su Yu (National Institute of Agricultural Sciences, RDA) ;
  • Yu-Mi Choi (National Institute of Agricultural Sciences, RDA) ;
  • Xiaohan Wang (National Institute of Agricultural Sciences, RDA) ;
  • Manjung Kang (National Institute of Agricultural Sciences, RDA)
  • 유동수 (농촌진흥청 국립농업과학원) ;
  • 최유미 (농촌진흥청 국립농업과학원) ;
  • 왕샤오한 (농촌진흥청 국립농업과학원) ;
  • 강만정 (농촌진흥청 국립농업과학원)
  • Received : 2023.05.04
  • Accepted : 2023.06.08
  • Published : 2023.08.01
Download PDF
⟨ Previous Next ⟩

Abstract

Developing and breeding improved legume-based food resources require collecting useful genetic traits with heritability even though requiring some time-consuming, costly, and labor intensive. We attempted to infer heritability of nine genetic traits-days to flowering, days to maturity, period from flowering to maturity, the number of seeds per pod, 100-seeds weight, and four contents such as crude protein, crude oil, crude fiber, and dietary fiber-using 455 homologous chloroplast gene sets of six species of legumes. Correlation analysis between genetic trait differences and phylogenetic distance of homologous gene sets revealed that days to flowering, the number of seeds per pod, and crude oil content were influenced by genetic factors rather than environmental factors by 62.86%, 69.45%, 57.14% of correlated genes (P-value ≤ 0.05) and days to maturity showed intermediate genetic effects by 62.42% (P-value ≤ 0.1). The period from flowering to maturity and 100-seeds weight showed different results compared to those of some previous studies, which may be attributed to highly complicated internal (epistatic or additive gene effects) and external effects (cultural environment and human behaviors). Despite being slightly unexpected, our results and method can widely contribute to analyze heritability by including genetic information on mitochondria, nuclear genome, and single nucleotide polymorphisms.

두류는 식량으로서 중요한 자원 중의 하나로 유용한 형질을 이용하여 장기적인 먹거리의 소재로 개발 및 활용하고 있다. 그런데 형질은 작물의 다양성과 관련하여 유전적 혹은 환경적 요인에 따라 형질 변이가 발생하기 때문에 유용한 형질의 장기적인 활용을 위해서는 유전적으로 장기적인 유지가 가능한 유전력이 높은 형질을 선발하는 것이 중요하다. 그러나 유전력의 추정은 복잡한 세대증식의 설계와 재배시간, 농업노동력 공급 등에 필요한 많은 시간과 비용이 소요되기 때문에 이를 해결할 수 있는 대안이 요구된다. 본 연구에서는 두류 6종에 대한 형태적 형질과 엽록체의 총455개 유전자의 계통 분류학적 차이를 통계적으로 상호 비교하여 형질에 대한 유전력을 추정하였다. 그 결과로 개화일수, 협당 립수, 조지방이 유의수준 0.05 이하(P-value≤0.05)에서 상관관계가 있는 유전자가 각각 62.86%, 69.45%, 57.14%로 높은 상관성을 보였고, 생육일수는 유의수준 0.1 이하에서 62.42%로 상관성을 보임으로써 환경적 영향보다 유전적 영향에 의한 변이가 더 크게 작용할 것으로 예상된다. 반면 성숙일수, 100립중, 조단백질, 조섬유, 식이섬유 함량에 대한 변이는 유의수준 0.05이하에서 상관성이 있는 유전자가 평균 11.82%로 환경적 변화영향이 더 클 것으로 추정되었다. 이 가운데 성숙일수와 100립중은 기존의 연구와는 다른 결과를 보였는데 이는 재배환경, 인간활동(농약, 비료 사용 등)과 같은 환경적 영향 뿐만아니라 유전력과 유전적 진전과의 관계에 따른 상위적, 상가적 유전자의 복잡한 영향으로 인하여 다른 연구결과가 나타났을 것으로 판단된다. 비록 엽록체 유전자 정보를 이용한 유전력 추정이 다소 미흡하지만 향 후에 단일염기다형성의 활용, 낮은 계통발생 신호의 보완을 위한 미토콘드리아 유전체 정보, 핵DNA 유전자 정보 등을 활용하고, 실제 조사결과와의 비교검정을 통한 보완이 이루어진다면 유전력 추정을 통한 신품종 개발 및 우수자원 선발과 육종기술 등과 같이 농업유전자원의 보존, 관리, 재배, 증식 등 광범위한 농업분야의 발전에 크게 기여할 수 있을 것이다.

Keywords

Acknowledgement

본 연구는 농촌진흥청 국립농업과학원 연구과제 '농업유전자원 정보관리 체계 및 다양성 분석시스템 구축(PJ017274)'의 지원을 받아 수행하였습니다.

References

  1. Ackerly, D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proc. Natl. Acad. Sci. 106:19699-19706. https://doi.org/10.1073/pnas.0901635106
  2. Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215(3):403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  3. Avila-Lovera, E., K. Winter and G.R. Goldsmith. 2023. Evidence for phylogenetic signal and correlated evolution in plant-water relation traits. New Phytol. 237(2):392-407. https://doi.org/10.1111/nph.18565
  4. Beavis, W., L. Merrick, K. Meade, A. Campbell, D. Muenchrath and S.-Z. Fei. 2021. Inheritance of Quantitative Traits. Plant Breeding E-Learning in Africa, Ames, IW (USA). pp. 1-64.
  5. Bekele, A., G. Alemaw and H. Zeleke. 2012. Genetic divergence among soybean (Glycine max (L) Merrill) introductions in ethiopia based on agronomic traits. Journal of Biology, Agriculture and Healthcare 2(6):6-12.
  6. Bista, P., S. Thapa, S. Rawal, D. Dhakal and D. Joshi. 2022. Agro-morphological characterization and estimation of genetic parameters of spring maize hybrids in the inner plains of far-west Nepal. Int. J. Agron. 2022:4806266.
  7. Blomberg, S.P., T. Garland JR. and A.R. Ives. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57(4):717-745.
  8. Carver, T., S.R. Harris, M. Berriman, J. Parkhill and J.A. McQuillan. 2011. Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28(4):464-469. https://doi.org/10.1093/bioinformatics/btr703
  9. Chandrawat, K.S., K. Baig, S. Hashmi, D. Sarang, A. Kumar and P.K. Dumai. 2017. Study on genetic variability, heritability and genetic advance in soybean. Int. J. Pure. Appl. Biosci. 5(1):57-63. https://doi.org/10.18782/2320-7051.2592
  10. Cho, J.-W., S.-Y. Lee, S.-K. Kang and C.S. Kim. 2006. Yield and ecological characteristics of soybean in drained-paddy field. Korean J. Agric. Sci. 33(2):141-147 (in Korean).
  11. Choi, Y.-M., S. Lee, M.-C. Lee, S. Oh, O. Hur, G.T. Cho, M. Yoon and D.Y. Hyun. 2018. Comparison of agricultural traits and physicochemical properties of lentil (Lens culinaris Med.), chickpea (Cicer aretinum L.), and guar (Cyamopsis tetragonoloba L.) germplasms collected from tropical and subtropical regions. Korean J. Breed. Sci. 50(4):453-462 (in Korean). https://doi.org/10.9787/KJBS.2018.50.4.453
  12. Dobrogojski, J., M. Adamiec and R. Lucinski. 2020. The chloroplast genome: A review. Acta. Physiol. Plant. 42(6):98.
  13. Escribano, M.R., M. Santalla and A.M. de Ron. 1997. Genetic diversity in pod and seed quality traits of common bean populations from northwestern Spain. Euphytica 93(1):71-81. https://doi.org/10.1023/A:1002908224793
  14. Galperin, M.Y., Y.I. Wolf, K.S. Makarova, R. Vera Alvarez, D. Landsman and E.V. Koonin. 2020. COG database update: Focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 49(D1):D274-D281.
  15. Goncalves, D.J.P., B.B. Simpson, E.M. Ortiz, G.H. Shimizu and R.K. Jansen. 2019. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol. Phylogen. Evol. 138:219-232. https://doi.org/10.1016/j.ympev.2019.05.022
  16. Guillen-Escriba, C., F.D. Schneider, B. Schmid, A. Tedder, F. Morsdorf, R. Furrer, A. Hueni, P.A. Niklaus and M.E. Schaepman. 2021. Remotely sensed between-individual functional trait variation in a temperate forest. Ecol. Evol. 11(16):10834-10867. https://doi.org/10.1002/ece3.7758
  17. Holland, J.B., W.E. Nyquist and C.T. Cervantes-Martinez. 2003. Estimating and interpreting heritability for plant breeding: An update. Plant Breed. Rev. 22:9-112.
  18. Jansen, R.K., M.F. Wojciechowski, E. Sanniyasi, S.-B. Lee and H. Daniell. 2008. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpp intron losses among legumes (Leguminosae). Mol. Phylogen. Evol. 48(3):1204-1217. https://doi.org/10.1016/j.ympev.2008.06.013
  19. Jeong, J.Y. and C. Jo. 2018. The application of meat alternatives and ingredients for meat and processed meat industry. Food Sci. Anim. Resour. 7(1):2-11 (in Korean).
  20. Jiang, G.-L., L.K. Rutto, S. Ren, R.A. Bowen, H. Berry and K. Epps. 2018a. Genetic analysis of edamame seed composition and trait relationships in soybean lines. Euphytica 214:1-10. https://doi.org/10.1007/s10681-017-2087-x
  21. Jiang, G.-L., P. Chen, J. Zhang, L. Florez-Palacios, A. Zeng, X. Wang, R.A. Bowen, A. Miller and H. Berry. 2018b. Genetic analysis of sugar composition and its relationship with protein, oil, and fiber in soybean. Crop. Sci. 58(6):2413-2421. https://doi.org/10.2135/cropsci2018.03.0173
  22. Jibril, S. 2019. Genetic variability and association of yield, nutritional quality and yield related traits in large seeded common bean (Phaseolus vulgaris L.) varieties at Haramaya, Eastern Ethiopia. Haramaya University, Haramaya, Ethiopia. pp. 1-60.
  23. Jung, K.H., C.Y. Gu, L.Y. Tae, K.H. Soon, E.M. Young and S.J. Uk. 1999. Detection of putative qtl conferring grain size and shape in rice. Korean J. Breed. Sci. 31(4):330-335 (in Korean).
  24. Khan, M.M.H., M.Y. Rafii, S.I. Ramlee, M. Jusoh and A. Mamun. 2020. Genetic variability, heritability, and clustering pattern exploration of bambara groundnut (Vigna subterranea L. Verdc) accessions for the perfection of yield and yield-related traits. Biomed. Res. Int. 2020:2195797.
  25. Kim, H.-K., H.-N. Lim, Y.-W. Choi, J.-S. Kang, Y.-J. Lee, Y.-H. Park, J.-M. Suh and B.-G. Son. 2013. Identification of quantitative trait loci associated with number of pod per plant, number of seed per plant, number of seed per pod in soybean (Glycine max L). J. Agric. Life Sci. 47(5):1-9 (in Korean). https://doi.org/10.14397/jals.2013.47.6.1
  26. Kim, H.T., J.M. Ko, I.Y. Baek, W.Y. Han, H.T. Yun, B.W. Lee, S.O. Shin, J.H. Seo, H.S. Kim and D.Y. Kwak. 2019. 'Neulchan', a middle-seed, disease-resistant, and high-yield soybean cultivar for soy-paste and tofu. Korean J. Breed. Sci. 51(4):475-481 (in Korean). https://doi.org/10.9787/KJBS.2019.51.4.475
  27. Kumar, P., S. Bishnoi and P. Kaushik. 2017. Genetic variability, heritability and genetic advance for seed yield and other agro-morphological traits in faba bean (Vicia faba L.) genotypes of different origin. Trends Biosci. 10(4):1246-1248.
  28. Lee, J.J. 2011. Colored foods and diabetes. J. Korean Diabetes. 12(4):219-224 (in Korean). https://doi.org/10.4093/jkd.2011.12.4.219
  29. Lee, S.-Y., J.-w. Kang, S.-h. Wang, T.-c. Park, J.-W. Chung and Y.-S. So. 2021. Evaluation of regional adaptability in introduced super sweet corn hybrids and heritability of agronomic traits. Korean J. Crop. Sci. 66(2):130-137 (in Korean).
  30. Leleji, O.I., M.H. Dickson, L.V. Crowder and J.B. Bourke. 1972. Inheritance of crude protein percentage and its correlation with seed yield in beans, Phaseolus Vulgaris L. Crop Sci. 12(2):cropsci1972.0011183X001200020004x.
  31. Lipka, A.E., F. Tian, Q. Wang, J. Peiffer, M. Li, P.J. Bradbury, M.A. Gore, E.S. Buckler and Z. Zhang. 2012. Gapit: Genome association and prediction integrated tool. Bioinformatics 28(18):2397-2399. https://doi.org/10.1093/bioinformatics/bts444
  32. Mesfin, T., M. Wassu and J. Mussa. 2021. Variation in genetic variability and heritability of agronomic traits in faba bean (Vicia faba L.) genotypes under soil acidity stress evaluated with and without lime in Ethiopia. Afr. J. Agric. Res. 17(2):355-364. https://doi.org/10.5897/AJAR2020.15128
  33. Neelima, G., S. Mehtre and G. Narkhede. 2018. Genetic variability, heritability and genetic advance in soybean. Int. J. Pure. Appl. Biosci. 6(2):1011-1017. https://doi.org/10.18782/2320-7051.5982
  34. Nge, F.J., E. Biffin, K.R. Thiele and M. Waycott. 2021. Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the australian plant genus adenanthos (proteaceae). Front. Ecol. Evol. 8(616741):1-15.
  35. O'Leary, N.A., M.W. Wright, J.R. Brister, S. Ciufo, D. Haddad, R. McVeigh, B. Rajput, B. Robbertse, B. Smith-White, D. Ako-Adjei, A. Astashyn, A. Badretdin, Y. Bao, O. Blinkova, V. Brover, V. Chetvernin, J. Choi, E. Cox, O. Ermolaeva, C.M. Farrell, T. Goldfarb, T. Gupta, D. Haft, E. Hatcher, W. Hlavina, V.S. Joardar, V.K. Kodali, W. Li, D. Maglott, P. Masterson, K.M. McGarvey, M.R. Murphy, K. O'Neill, S. Pujar, S.H. Rangwala, D. Rausch, L.D. Riddick, C. Schoch, A. Shkeda, S.S. Storz, H. Sun, F. Thibaud-Nissen, I. Tolstoy, R.E. Tully, A.R. Vatsan, C. Wallin, D. Webb, W. Wu, M.J. Landrum, A. Kimchi, T. Tatusova, M. DiCuccio, P. Kitts, T.D. Murphy and K.D. Pruitt. 2015. Reference sequence (refseq) database at ncbi: Current status, taxonomic expansion, and functional annotation. Nucleic. Acids. Res. 44(D1):D733-D745.
  36. Palmer, J.D. 1985. Chloroplast DNA and molecular phylogeny. Bioessays 2(6):263-267. https://doi.org/10.1002/bies.950020607
  37. Park, H.-S. and C.-H. Jun. 2009. A simple and fast algorithm for k-medoids clustering. Expert Syst. Appl. 36(2):3336-3341 (in Korean). https://doi.org/10.1016/j.eswa.2008.01.039
  38. Park, J., H. Xi and S.-h. Oh. 2020a. Comparative chloroplast genomics and phylogenetic analysis of the viburnum dilatatum complex (adoxaceae) in Korea. Korean J. Pl. Taxon. 50(1):8-16 (in Korean). https://doi.org/10.11110/kjpt.2020.50.1.8
  39. Park, K.-s., J.-h. Lee, G.-t. Cho, Y.-m. Choi, B.-s. Hahn, M.-s. Yoon, Y.-s. Lee and J.-y. Yi. 2020b. Status of research of conservation and utilization for plant genetic resources of national agrobiodiversity center in Korea. The Korean Society for Seed Science & Industry 16(2):44-49 (in Korean).
  40. Revelle, W. and M.W. Revelle. 2022. Package 'psych'. The comprehensive R archive network. The Comprehensive R Archive Network. Vienna, Austria. pp. 1-465.
  41. Rimlinger, A., N. Raharimalala, V. Letort, J.-J. Rakotomalala, D. Crouzillat, R. Guyot, P. Hamon and S. Sabatier. 2020. Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar. Ann. Bot. 126(5):849-863. https://doi.org/10.1093/aob/mcaa073
  42. Rivas, J.D.L., J.J. Lozano and A.R. Ortiz. 2002. Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome. Res. 12(4):567-583. https://doi.org/10.1101/gr.209402
  43. Rosbakh, S. 2014. Effects of climate change on alpine vegetation-functional analysis as a basis for prediction, Ph. D. Thesis, Regensburg Univ., Regensburg, German. p. 1-156.
  44. Seo, M.-J., M.R. Park, H.T. Yun and C.H. Park. 2017. Analysis on variation and stability of agricultural characteristics in soybean landraces and cultivars. J. Korean Soc. Int. Agric. 29(3):271-281 (in Korean). https://doi.org/10.12719/KSIA.2017.29.3.271
  45. Seo, M.-S., C. Cho, N. Jeong, S.-K. Sung, M.-S. Choi, M. Jin and D.-Y. Kim. 2021. In vitro tissue culture frequency and transformation of various cultivars of soybean (Glycine max (L.) Merr.). Korean J. Plant Res. 34:278-286 (in Korean).
  46. Sharifi, P., H. Astereki and M. Pouresmael. 2018. Evaluation of variations in chickpea (Cicer arietinum L.) yield and yield components by multivariate technique. Ann. Agrar. Sci. 16(2):136-142. https://doi.org/10.1016/j.aasci.2018.02.003
  47. Sievers, F. and D.G. Higgins. 2018. Clustal omega for making accurate alignments of many protein sequences. Protein Sci. 27(1):135-145. https://doi.org/10.1002/pro.3290
  48. Sim, S., J.-S. Kim, D.-P. Jin, W. Lee, C.W. Hyun and J.-H. Kim. 2022. New record for alien plant, Urtica dioica L. (Urticaceae) in Korea. Korean J. Plant Res. 35(1):100-108 (in Korean).
  49. Sousa, F., P. Civan, P.G. Foster and C.J. Cox. 2020. The chloroplast land plant phylogeny: Analyses employing better-fitting tree- and site-heterogeneous composition models. Front. Plant Sci. 11:1-10. https://doi.org/10.3389/fpls.2020.01062
  50. Sveinsson, S. and Q. Cronk. 2016. Conserved gene clusters in the scrambled plastomes of irlc legumes (Fabaceae: Trifolieae and Fabeae). bioRxiv:040188.
  51. Tian, S., P. Lu, Z. Zhang, J.Q. Wu, H. Zhang and H. Shen. 2021. Chloroplast genome sequence of chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. BMC Genomics. 22(1):194.
  52. Toker, C. 2004. Estimates of broad-sense heritability for seed yield and yield criteria in faba bean (Vicia faba L.). Hereditas 140(3):222-225. https://doi.org/10.1111/j.1601-5223.2004.01780.x
  53. Tola, M., B. Tesso and B. Amsalu. 2023. Genetic variability and association of yield and yield-related traits under moisture stress in common bean genotypes (Phaseolus vulgaris L.) at Melkassa and Miesso, Ethiopia. Adv. Agric. 2023:8697497.
  54. Yaradua, S.S. and D.A. Alzahrani. 2019. Chloroplast genome: An important tool for inferring phylogenetic relationship. J. Bio. & Env. Sci. 15(1):95-101.
  55. Yassin, A., N. Gidaszewski, V. Debat and J.R. David. 2022. Long-term evolution of quantitative traits in the drosophila melanogaster species subgroup. Genetica 150(6):343-353. https://doi.org/10.1007/s10709-022-00171-9
  56. Younis, N., M.A. Hanif, S. Sadiq, G. Abbas, M.J. Asghar and M.A. Haq. 2008. Estimates of genetic parameters and path analysis in lentil (Lens culinaris Medik). Pak. J. Agri. Sci. 45(3):44-48.
  57. Yue, Y., J. Li, X. Sun, Z. Li and B. Jiang. 2023. Polymorphism analysis of the chloroplast and mitochondrial genomes in soybean. BMC Plant Biol. 23(1):15.