True hybridity analysis using genome-wide hypervariable SSR markers in pomegranate
Vol 7, Issue 1, 2024
VIEWS - 300 (Abstract) 153 (PDF) 86 (Supp. file)
Abstract
A total of 25 SSR primers were screened on 37 putative F1s derived from the five different crosses. Identified cross specific highly informative SSRs primers, i.e., 14 for the first cross, 10 for the second, 12 for the third and 6 each for fourth and fifth crosses. For the first cross Bhagwa × Daru 17, four primers (HvSSRT_375, NRCP_SSR9, NRCP_SSR12 and NRCP_SSR92) were found to be highly informative with higher 100% hybrid purity index (HPI), PIC (~0.52), and observed heterozygosity (Ho, range 0.87–0.93) values, and two F1s namely H1 and H2 were found to be highly heterotic with a heterozygosity index (HI) of 92.85%. Similarly, for Bhagwa × Nana, three primers (HvSSRT_375, HvSSRT_605 and NRCP_SSR19) had higher HPI (70%–100%), PIC (0.52–0.69), and Ho (0.75–0.33) values, and three F1s H1, H2, and H4 had 70% (HI). For Bhagwa × IC318712, four SSRs (HvSSRT_254, HvSSRT_348, HvSSRT_826 and NRCP_SSR95) had higher Ho (~0.83), HPI (100%) and PIC (~0.52) values, and four F1s H2, H7, H9, and H10 showed 91.66% (HI). For Bhagwa × Nayana, HvSSRT_605, HvSSRT_826, and HvSSRT_432, and for Ganesh × Nayana, HVSSRT_375, HVSSRT_605, and HvSSRT_826 were found informative. These markers will be highly useful in developing maps of populations.
Keywords
References
1. Holland D, Bar-Ya’akov I. Pomegranate: aspects concerning dynamics of health beneficial phytochemicals and therapeutic properties with respect to the tree cultivar and the environment. In: Yaniv Z, Dudai N (editors). Medicinal and Aromatic Plants of the Middle-East. Springer Netherlands; 2014. doi: 10.1007/978-94-017-9276-9
2. Bar-Ya’akov I, Tian L, Amir R, et al. Primary Metabolites, Anthocyanins, and Hydrolyzable Tannins in the Pomegranate Fruit. Frontiers in Plant Science. 2019; 10. doi: 10.3389/fpls.2019.00620
3. Ophir R, Sherman A, Rubinstein M, et al. Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity. PLoS ONE. 2014; 9(2): e88998. doi: 10.1371/journal.pone.0088998
4. Bellesia A, Verzelloni E, Tagliazucchi D. Pomegranate ellagitannins inhibit α-glucosidase activityin vitroand reduce starch digestibility under simulated gastro-intestinal conditions. International Journal of Food Sciences and Nutrition. 2014; 66(1): 85-92. doi: 10.3109/09637486.2014.953455
5. Aslan A, Can M, Boydak D. Anti-Oxidant effects of pomegranate juice on Saccharomyces cerevisiae cell growth. African Journal of Traditional, Complementary and Alternative Medicines. 2014; 11(4): 14. doi: 10.4314/ajtcam.v11i4.3
6. Ahmed MM, Samir ESA, El-Shehawi AM, et al. Anti-obesity effects of Taif and Egyptian pomegranates: molecular study. Bioscience, Biotechnology, and Biochemistry. 2015; 79(4): 598-609. doi: 10.1080/09168451.2014.982505
7. NHB. Available online: http://nhb.gov.in/PDFViwer.aspx?Enc=3ZOO8K5CzcdC/Yq6HcdIxC0U1kZZenFuNVXacDLxz28 (accessed on 20 August 2020).
8. Jalikop SH, Rawal RD, Kumar R. Exploitation of sub-temperate pomegranate Daru in breeding tropical varieties. Acta Horticulturae. 2005; (696): 107-112. doi: 10.17660/actahortic.2005.696.18
9. Ravishankar KV, Chaturvedi K, Puttaraju N, et al. Mining and characterization of SSRs from pomegranate (Punica granatum L.) by pyrosequencing. Plant Breeding. 2015; 134(2): 247-254. doi: 10.1111/pbr.12238
10. Patil PG, Singh NV, Parashuram S, et al. Genome-wide characterization and development of simple sequence repeat markers for genetic studies in pomegranate (Punica granatum L.). Trees. 2020; 34(4): 987-998. doi: 10.1007/s00468-020-01975-y
11. Patil PG, Singh NV, Parashuram S, et al. Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate (Punica granatum L.). Physiology and Molecular Biology of Plants. 2020; 26(4): 683-696. doi: 10.1007/s12298-020-00790-6
12. Ono NN, Britton MT, Fass JN, et al. Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery. Journal of Integrative Plant Biology. 2011; 53(10): 800-813. doi: 10.1111/j.1744-7909.2011.01073.x
13. Harel-Beja R, Sherman A, Rubinstein M, et al. A novel genetic map of pomegranate based on transcript markers enriched with QTLs for fruit quality traits. Tree Genetics and Genomes. 2015; 11(5). doi: 10.1007/s11295-015-0936-0
14. Trainin T, Harel-Beja R, Bar-Ya’akov I, et al. Fine Mapping of the “black” Peel Color in Pomegranate (Punica granatum L.) Strongly Suggests That a Mutation in the Anthocyanidin Reductase (ANR) Gene Is Responsible for the Trait. Frontiers in Plant Science. 2021; 12. doi: 10.3389/fpls.2021.642019
15. Di Guardo M, Tadiello A, Farneti B, et al. A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus domestica Borkh.). PLoS One. 2013; 8(10): e78004. doi: 10.1371/journal.pone.0078004
16. Olukolu BA, Trainin T, Fan S, et al. Genetic linkage mapping for molecular dissection of chilling requirement and budbreak in apricot (Prunus armeniaca L.). Genome. 2009; 52(10): 819-828. doi: 10.1139/g09-050
17. Fan S, Bielenberg DG, Zhebentyayeva TN, et al. Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica). New Phytologist. 2009; 185(4): 917-930. doi: 10.1111/j.1469-8137.2009.03119.x
18. Okoye MN, Singh R, Uguru MI, et al. Application of microsatellite markers for hybrid verification and genetic analysis of oil palm (Elaeis guineensis Jacq.). Nigerian Journal of Biotechnology. 2021; 37(2): 1-12. doi: 10.4314/njb.v37i2.1
19. Vincent K, Robert K, Morag F, et al. Identification of F1 Cassava (Manihot esculenta Crantz) Progeny Using Microsatellite Markers and Capillary Electrophoresis. American Journal of Plant Sciences. 2014; 5(1): 119-125. doi: 10.4236/ajps.2014.51015
20. Chi ZJ, Shan GY, Dong LZ, et al. Identification of the F1 hybrids of grape using SSR molecular markers. Journal of Shenyang Agricultural University. 2016; 47: 148-152.
21. Kumar K, Srivastav M, Singh S, et al. Ascertaining hybridity of progenies in mango (Mangifera indica L.) using microsatellite (SSR) markers. Journal of Agriculture and Ecology. 2016; 2(2): 1-10. doi: 10.53911/jae.2016.2201
22. Kaur K, Kumar K, et al. Allelic pattern of SSRs with high hybrid detection efficiency and inheritance of leaf petiole wing in interspecific Citrus crosses. Fruits. 2021; 76(1): 30-38. doi: 10.17660/th2021/76.1.4
23. Subashini V, Shanmugapriya A, Yasodha R. Hybrid purity assessment in Eucalyptus F1 hybrids using microsatellite markers. 3 Biotech. 2013; 4(4): 367-373. doi: 10.1007/s13205-013-0161-1
24. Patil PG, Jamma SM, Singh NV, et al. Assessment of genetic diversity and population structure in pomegranate (Punica granatum L.) using hypervariable SSR markers. Physiology and Molecular Biology of Plants. 2020; 26(6): 1249-1261. doi: 10.1007/s12298-020-00825-y
25. Patil PG, Singh NV, Bohra A, et al. Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome. Frontiers in Plant Science. 2021; 12. doi: 10.3389/fpls.2021.645055
26. Ravishankar KV, Anand L, Dinesh MR. Assessment of genetic relatedness among mango cultivars of India using RAPD markers. The Journal of Horticultural Science and Biotechnology. 2000; 75(2): 198-201. doi: 10.1080/14620316.2000.11511223
27. Bohra A, Dubey A, Saxena RK, et al. Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biology. 2011; 11(1). doi: 10.1186/1471-2229-11-56
28. Haynes KG, Zaki HEM, Christensen CT, et al. High Levels of Heterozygosity Found for 15 SSR Loci in Solanum chacoense. American Journal of Potato Research. 2017; 94(6): 638-646. doi: 10.1007/s12230-017-9602-4
29. Patella A, Scariolo F, Palumbo F, et al. Genetic Structure of Cultivated Varieties of Radicchio (Cichorium intybus L.): A Comparison between F1 Hybrids and Synthetics. Plants. 2019; 8(7): 213. doi: 10.3390/plants8070213
30. Jalikop SH, Venugopalan R, Kumar R. Association of fruit traits and aril browning in pomegranate (Punica granatum L.). Euphytica. 2010; 174(1): 137-141. doi: 10.1007/s10681-010-0158-3
31. Jalikop SH, Kumar PS, Rawal RD, et al. Breeding pomegranate for fruit attributes and resistance to bacterial blight. Indian Journal of Horticulture. 2006; 63(4): 352-358.
32. Bohra A, Pareek S, Jha R, et al. Modern genomic tools for pigeonpea improvement: status and prospects. In: Varshney RK, Saxena RK, Jackson SA, et al. The Pigeonpea Genome. Springer International Publishing; 2017. doi: 10.1007/978-3-319-63797-6
33. Corley RHV. Illegitimacy in oil palm breeding—A review. Journal of Oil Palm Research 2005; 17: 64-69.
34. Ben Romdhane M, Riahi L, Jardak R, et al. Fingerprinting and genetic purity assessment of F1 barley hybrids and their salt-tolerant parental lines using nSSR molecular markers. 3 Biotech. 2018; 8(1). doi: 10.1007/s13205-017-1080-3
35. Jansson S, Bhalerao R, Groover A, et al. Genetics and Genomics of Populus. Springer New York; 2010. doi: 10.1007/978-1-4419-1541-2
36. Nadeem M, Wang X, Akond M, et al. Hybrid identification, morphological evaluation and genetic diversity analysis of' Rosa x hybrid by SSR markers. Australian Journal of Crop Science 2014; 8(2): 183-190.
DOI: https://doi.org/10.24294/th.v7i1.3491
Refbacks
- There are currently no refbacks.
This work is licensed under a Creative Commons Attribution 4.0 International License.
This site is licensed under a Creative Commons Attribution 4.0 International License.