Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions.
Direct seeded rice
Early seedling vigour-related traits
Haplotype analysis
QTLs
Rice
Journal
Molecular biology reports
ISSN: 1573-4978
Titre abrégé: Mol Biol Rep
Pays: Netherlands
ID NLM: 0403234
Informations de publication
Date de publication:
Oct 2023
Oct 2023
Historique:
received:
03
04
2023
accepted:
26
07
2023
medline:
26
9
2023
pubmed:
9
8
2023
entrez:
9
8
2023
Statut:
ppublish
Résumé
The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
Sections du résumé
BACKGROUND
BACKGROUND
The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial.
METHODS AND RESULTS
RESULTS
In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2.
CONCLUSIONS
CONCLUSIONS
In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
Identifiants
pubmed: 37555871
doi: 10.1007/s11033-023-08714-9
pii: 10.1007/s11033-023-08714-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
8177-8188Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature B.V.
Références
Anandan A, Parameswaran C, Azharudheen TP, Singh ON (2018) Towards the development of dry direct-seeded rice varieties by stacking of multiple QTLs/genes. Oryza 55:51–56. https://doi.org/10.5958/2249-5266.2018.00006.1
doi: 10.5958/2249-5266.2018.00006.1
Zhang ZH, Qu XS, Wan S, Chen LH, Zhu YG (2005) Comparison of QTL controlling seedling vigor under different temperature conditions using recombinant inbred lines in rice (Oryza sativa). Ann Bot 95:423–429. https://doi.org/10.1093/aob/mci039
doi: 10.1093/aob/mci039
pubmed: 15574482
Zhang ZH, Su L, Li W, Chen W, Zhu YG (2005) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci J 168:527–534. https://doi.org/10.1016/j.plantsci.2004.09.021
doi: 10.1016/j.plantsci.2004.09.021
Mahender A, Anandan A, Pradhan SK (2015) Early seedling vigour, an imperative trait for direct-seeded rice: an overview on physio-morphological parameters and molecular markers. Planta 241(5):1027–1050. https://doi.org/10.1007/s00425-015-2273-9
doi: 10.1007/s00425-015-2273-9
pubmed: 25805338
Li X, Dong J, Zhu W (2023) Progress in the study of functional genes related to direct seeding of rice. Mol Breeding 43:46. https://doi.org/10.1007/s11032-023-01388-y
doi: 10.1007/s11032-023-01388-y
Diwan J, Channbyregowda M, Shenoy V, Salimath P, Bhat R (2013) Molecular mapping of early vigour related QTLs in rice. Res J Biol 1:24–30
Wang Z, Wang J, Bao Y, Wang F, Zhang H (2010) Quantitative trait loci analysis for rice seed vigor during the germination stage. J Zhejiang Univ Sci B 11(12):958–964. https://doi.org/10.1631/jzus.B1000238
doi: 10.1631/jzus.B1000238
pubmed: 21121075
pmcid: 2997405
Xie L, Tan Z, Zhou Y, Xu R, Feng L, Xing Y, Qi X (2014) Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice. J Integr Plant Biol 56:749–759. https://doi.org/10.1111/jipb.12190
doi: 10.1111/jipb.12190
pubmed: 24571491
Han L, Qiao Y, Zhang S, Zhang Y, Cao G, Kim J, Lee K, Koh H (2007) Identification of quantitative trait loci for cold response of seedling vigor traits in rice. J Genet Genomics 34(3):239–246. https://doi.org/10.1016/S1673-8527(07)60025-3
doi: 10.1016/S1673-8527(07)60025-3
pubmed: 17498621
Abe A, Takagi H, Fujibe T, Aya K, Kojima M, Sakakibara H, Uemura A, Matsuoka M, Terauchi R (2012) OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice. Theor Appl Genet 125(4):647–657. https://doi.org/10.1007/s00122-012-1857-z
doi: 10.1007/s00122-012-1857-z
pubmed: 22481119
Lv YS, Shao GN, Jiao GA, Sheng ZH, Xie LH, Hu SK, Tang SQ, Wei XG, Hu PS (2021) Targeted mutagenesis of POLYAMINE OXIDASE 5 that negatively regulates mesocotyl elongation enables the generation of direct-seeding rice with improved grain yield. Mol Plant 14(2):344–351. https://doi.org/10.1016/j.molp.2020.11.007
doi: 10.1016/j.molp.2020.11.007
pubmed: 33220510
He Y, Cheng J, He Y, Yang B, Cheng Y, Yang C, Zhang H, Wang Z (2019) Influence of isopropylmalate synthase OsIPMS 1 on seed vigour associated with amino acid and energy metabolism in rice. Plant Biotechnol J 17(2):322–337. https://doi.org/10.1111/pbi.12979
doi: 10.1111/pbi.12979
pubmed: 29947463
Sinha P, Singh VK, Saxena RK, Khan AW, Abbai R, Chitikineni A, Desai A, Molla J, Upadhyaya HD, Kumar A, Varshney RK (2020) Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnol J 18(12):2482–2490. https://doi.org/10.1111/pbi.13422
doi: 10.1111/pbi.13422
pubmed: 32455481
pmcid: 7680530
Abbai R, Singh VK, Nachimuthu VV, Sinha P, Selvaraj R, Vipparla AK, Singh AK, Singh UM, Varshney RK, Kumar A (2019) Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains. Plant Biotechnol J 17(8):1612–1622. https://doi.org/10.1111/pbi.13087
doi: 10.1111/pbi.13087
pubmed: 30701663
pmcid: 6662101
ISTA-International Seed Testing Association (2015) ISTA rules full issue. International Rules for Seed Testing 1–276
Abdul-Baki AA, Anderson JD (1973) Vigour determination in soybean seed by multiple criteria. Crop Sci 13:630–633. https://doi.org/10.2135/cropsci1973.0011183X001300060013x
doi: 10.2135/cropsci1973.0011183X001300060013x
Al-Jibouri HA, Miller PA, Robinson HF (1958) Genotypic and environmental variances and covariances in an upland Cotton cross of interspecific origin. Agron J 50(10):633–636. https://doi.org/10.2134/agronj1958.00021962005000100020x
doi: 10.2134/agronj1958.00021962005000100020x
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4325. https://doi.org/10.1093/nar/8.19.4321
doi: 10.1093/nar/8.19.4321
pubmed: 7433111
pmcid: 324241
Bhargavi M, Maneesha K, Withanawasam DM, Aratikatla KR, Himabindu S, Prashanth M, Shanthi P, Kommana ML, Reddy DM, Reddy BR, Vemireddy LR (2021) A novel barcode system for rapid identification of rice (Oryza sativa L.) varieties using agro-morphological descriptors and molecular markers. Mol Biol Rep 48(3):2209–2221. https://doi.org/10.1007/s11033-021-06230-2
doi: 10.1007/s11033-021-06230-2
pubmed: 33675464
Lin F, Lazarus EZ, Rhee SY (2020) QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants. G3 (Bethesda). 10(7):2411–2421. https://doi.org/10.1534/g3.120.401122
doi: 10.1534/g3.120.401122
pubmed: 32430305
pmcid: 7341141
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28(19):2537–9. https://doi.org/10.1093/bioinformatics/bts460
doi: 10.1093/bioinformatics/bts460
pubmed: 22820204
pmcid: 3463245
Hwang TY, Sayama TA, Takahashi MA, Takada YO, Nakamoto YU, Funatsuki HI et al (2009) High density integrated linkage map based on SSR markers in soybean. DNA Res 16(4):213–225. https://doi.org/10.1093/dnares/dsp010
doi: 10.1093/dnares/dsp010
pubmed: 19531560
pmcid: 2725787
Barik J, Kumar V, Lenka SK, Panda D (2019) Genetic potentiality of lowland indigenous indica rice (Oryza sativa L.) landraces to anaerobic germination potential. Int J Curr Microbiol Appl Sci 8(12):2527–2538
doi: 10.20546/ijcmas.2019.812.296
Perrier X (2006) DARwin software. http://darwin.cirad.fr/darwin .
Voorrips RE (2002) Map Chart: Software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78. https://doi.org/10.1093/jhered/93.1.77
doi: 10.1093/jhered/93.1.77
pubmed: 12011185
Eliades NG, Eliades DG (2009) Haplotype analysis: Software for analysis of haplotype data. Forest Genetics and Forest Tree Breeding, Georg-August University Goettingen, Germany. URL http://www.uni-goettingen.de/en/134935.html
Manohara KK, Morajkar S, Shanbhag Y, Phadte P, Singh NK (2021) Haplotype analysis of Saltol QTL region in diverse landraces, wild rice and introgression lines of rice (Oryza sativa L.). Plant Genet Resour 19(4):289–298. https://doi.org/10.1017/s1479262121000320
doi: 10.1017/s1479262121000320
Xu L, Guo L, You H, Zhang O, Xiang X (2019) Novel haplotype combinations reveal enhanced seedling vigor traits in rice that can accurately predict dry biomass accumulation in seedlings. Breed Sci 69(4):651–657. https://doi.org/10.1270/jsbbs.19087
doi: 10.1270/jsbbs.19087
pubmed: 31988629
pmcid: 6977453
Menard G, Sandhu N, Anderson D, Catolos M, Hassall KL, Eastmond PJ, Kumar A, Kurup S (2021) Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice. Genomics 113(6):4227–4236. https://doi.org/10.1016/j.ygeno.2021.11.006
doi: 10.1016/j.ygeno.2021.11.006
pubmed: 34774680