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Mapping of QTLs for flood tolerance in rice using recombinant inbred lines of Indra and a new plant genetic resource AC 39416 A

Published online by Cambridge University Press:  22 March 2023

M. Girija Rani Open the ORCID record for M. Girija Rani [Opens in a new window] ,
P. V. Satyanarayana ,
N. Chamundeswari ,
P. V. Ramana Rao ,
M. Prabhakar ,
B. N. V. S. R. Ravikumar ,
P. Nagakumari  and
K. Kalpana
M. Girija Rani*
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
P. V. Satyanarayana
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
N. Chamundeswari
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
P. V. Ramana Rao
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
M. Prabhakar
Affiliation:
Central Institute of Dry land Agriculture, Hyderabad, Telangana, India
B. N. V. S. R. Ravikumar
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
P. Nagakumari
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
K. Kalpana
Affiliation:
Acharya N G Ranga Agricultural University, Regional Agricultural Research Station, Maruteru-534122, West Godavari District, AP, India
*
Author for correspondence: M. Girija Rani, E-mail: girijaaprri@gmail.com, m.girijarani@angrau.ac.in
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Abstract

Rice crop is affected by different types of floods at different stages of the crop cycle. Constant efforts of researchers resulted in the development of rice varieties for anaerobic germination, flash floods and stagnant flooding by both conventional and molecular breeding approaches. Detection of QTLs for different types of floods in new genetic source (AC39416A) is needed to combat adverse effects of climate change. Present investigation was carried out to identify QTLs for flood tolerance using recombinant inbred lines derived from Indra and AC39416A. QTL mapping resulted in identification of QTLs, qAG3.1 on chromosome 3 for anaerobic germination and qSF10.1 on chromosome 10 for plant survival % under stagnant flooding. These QTLs explain 59.08 and 13.21% of phenotypic variance respectively. Two candidate genes were identified in qAG3.1 region, LOC_Os03g42130 gibberellin 20 oxidase2 and LOC_Os03g44170 glutathione S-transferase. The underlying mechanism might be the inhibition of gibberellic acid synthesis and thereby protecting seedlings from oxidative stress under anoxia condition. Genomic region of qSF10.1 revealed LOC_Os10g35020 glycosyltransferase and LOC_Os10g35050 aquaporin protein loci, which might be responsible for adaptive mechanism for plant survival % under stagnant flooding. This indicates that the new genetic resource AC39416A has an ability to adopt to different types of flood tolerance in response to environmental stress. Unveiling physiological and molecular mechanisms for flood tolerance in AC39416A using advanced omics studies would help in precise genomic selections for sustained production in flood-prone areas.

Keywords

Flood tolerancelociQTL mappingriceRILs
Type
Research Article
Information
Plant Genetic Resources , Volume 20 , Issue 4 , August 2022 , pp. 270 - 276
Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of NIAB

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References

Aditi, B, Pawan, J, Neera, Y, Renu, S, Yashi, S, Balwant, S, Nisha, S, Sangeeta, S, Amitha, S, Vandna, R, Satish, V, Ramana Rao, PV, Girija Rani, M, Anuradha, T, Satyanarayana, PV, Krishnamurthy, SL, Prabodh, S, Deepika Singh, PK, Nilanjay, , Kumar, R, Sanjay, Ch, Ahmad, T, Mayank, R, Jawahar, K, Marandi, B, Padmini, S, Sarkar, RK, Singh, DP, Reddy, JN, Nimai, M, Paramsivam, K, Nadarajan, S, Thirumeni, S, Jyothi, B, Padmavathi, G, Ram, T and Singh, NK (2019) Genomics-assisted backcross breeding for infusing climate resilience in high-yielding green revolution varieties of rice. Indian Journal of Genetics and Plant Breeding 79 (Suppl), 160–170.Google Scholar
Agbeleye, OA, Olubiyi, MR, Ehirim, BO, Shittu, AO, Jolayemi, OL, Adetimirin, VO, Ariyo, OJ, Sanni, KA and Venuprasad, R (2019) Screening African rice (O. glaberrima Steud.) for tolerance to abiotic stress III Flooding. SABRAO Journal of Breeding and Genetics 51, 128–150.Google Scholar
Ahmed, F, Rafii, MY, Ismail, MZ, Abdul, SJ, Rahim, HA, Tanweer, FA and Latif, MA (2016) Recurrent parent genome recovery in different populations with the introgression of Sub1 gene from a cross between MR219 and Swarna-Sub1. Euphytica 207, 605–618.10.1007/s10681-015-1554-5CrossRefGoogle Scholar
Angaji, SA (2008) Mapping QTLs for submergence tolerance during germination in rice. African Journal of Biotechnology 7, 2551–2558.Google Scholar
Angaji, S, Septiningsih, EM, Mackill, DJ and Ismail, AM (2010) QTLs associated with tolerance of anaerobic conditions during germination in rice (Oryza sativa L.). Euphytica 172, 159–168.10.1007/s10681-009-0014-5CrossRefGoogle Scholar
Ara, A, Uddin, ABMA, Iftekharuddaula, KM, Saikat, MMH and Khan, MAI (2015) Introgression of Sub1 QTL into a rainfed lowland rice variety of Bangladesh using marker-assisted backcross approach. International Journal of Research 2, 233–244.Google Scholar
Baltazar, MD, Ignacio, JCI, Thomson, MJ, Ismail, AM and Septiningsih, EM (2014) QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping. Euphytica 197, 251–260.10.1007/s10681-014-1064-xCrossRefGoogle Scholar
Baltazar, MD, Ignacio, JCI, Thomson, MJ, Ismail, AM, Mendioro, MS and Septiningsih, EM (2019) QTL mapping for tolerance to anaerobic germination in rice from IR64 and the aus landrace Kharsu 80A. Breeding Science 69, 227–233.10.1270/jsbbs.18159CrossRefGoogle ScholarPubMed
Barik, J, Kumar, V, Lenka, SK and Panda, D (2020) An assessment of variation in morpho-physiological traits and genetic diversity in relation to submergence tolerance of five indigenous landraces of lowland rice. Rice Science 27, 32–43.CrossRefGoogle Scholar
Chattopadhyay, K, Chakraborty, K, Samal, P and Sarkar, RK (2021) Identification of QTLs for stagnant flooding tolerance in rice employing genotyping by sequencing of a RIL population derived from Swarna × Rashpanjor. Physiology and Molecular Biology of Plants 27, 2893–2909.10.1007/s12298-021-01107-xCrossRefGoogle ScholarPubMed
Gaspar, M, Bousser, A, Sissoëff, I, Roche, O, Hoarau, J and Mahé, A (2003) Cloning and characterization of ZmPIP1-5b, an aquaporin transporting water and urea. Plant Science 165, 21–31.10.1016/S0168-9452(03)00117-1CrossRefGoogle Scholar
Girijarani, M, Suryanarayana, Y, Satyanarayana, PV, Ramana Rao, PV, Prasad, KSN, Neerajakshi, Ch, Chamundeswari, N and Ravikumar, BNVSR (2013) Screening of rice genotypes for anaerobic germination. In Extended Summaries of ARRW Golden Jubilee International Symposium, India: Cuttack, p. 240.Google Scholar
Girijarani, M, Satyanarayana, PV, Suryanarayana, Y, Ramanarao, PV, Neerajakshi, C, Chamundeswari, N, Ravikumar, BNSVR, Pavani, SL, Kondayya, K, Ratnasree, P, Vishnuvardhan, KM, Sivaramprasad, K and Reddy, AV (2015) Enhancement of flood tolerance in a high yielding rice variety ‘Amara’ by marker assisted selection. SABRAO Journal of Breeding Genetics 47, 439–447.Google Scholar
Gonzaga, ZJ, Carandang, J, Sanchez, DL, Mackill, DJ and Septiningsih, EM (2016) Mapping additional QTLs from FR13A to increase submergence tolerance beyond SUB1. Euphytica 209, 627–636.10.1007/s10681-016-1636-zCrossRefGoogle Scholar
Gonzaga, ZJ, Carandang, J, Anshuman, S, Collard, BCY, Thomson, MJ and Septiningsih, EM (2017) Mapping QTLs for submergence tolerance in rice using a population fixed for SUB1A tolerant allele. Molecular Breeding 37, 47.10.1007/s11032-017-0637-5CrossRefGoogle Scholar
Hanba, YT, Shibasaka, M, Hayashi, Y, Hayakawa, T, Kasamo, K, Terashima, I and Katsuhara, M (2004) Overexpression of the barley aquaporin HvPIP2;1 increases internal CO2 conductance and CO2 assimilation in the leaves of transgenic rice plants. Plant Cell Physiology 45, 521–529.10.1093/pcp/pch070CrossRefGoogle ScholarPubMed
Iftekharuddaula, KM, Ahmed, HU, Ghosal, S, Moni, ZH, Amin, A and Ali, MD (2015) Development of new submergence tolerant rice variety for Bangladesh using marker-assisted backcrossing. Rice Science 22, 16–26.10.1016/j.rsci.2015.05.003CrossRefGoogle Scholar
Iftekharuddaula, KM, Ahmed, HU, Ghosal, S, Amin, A, Moni, ZR, Bisnu, PR, Hirendra, NB, Siddiquea, MA, Collard, BCY and Septiningsih, EM (2016) Development of early maturing submergence-tolerant rice varieties for Bangladesh. Field Crop Research 6594, 10.Google Scholar
Jain, M, Ghanashyam, C and Annapurna, B (2010) Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics 11, 73.10.1186/1471-2164-11-73CrossRefGoogle ScholarPubMed
Jeong, JM, Cho, YC and Jeong, JU (2020) QTL mapping and effect confirmation for anaerobic germination tolerance derived from the japonica weedy rice landrace PBR. Plant Breeding 139, 83–92.10.1111/pbr.12753CrossRefGoogle Scholar
Kato, Y, Collard, BCY, Septiningsih, EM and Ismail, AM (2014) Physiological analyses of traits associated with tolerance of long-term partial submergence in rice. AoB Plants 6, plu058.10.1093/aobpla/plu058CrossRefGoogle ScholarPubMed
Khanh, TD, Linh, LH, Linh, TH, Ham, LH and Xuan, TD (2013) Rapid and high-precision marker assisted backcrossing to introgress the SUB1 QTL into the Vietnamese elite rice variety. Journal of Plant Breeding Crop Science 5, 26–33.10.5897/JPBCS12.052CrossRefGoogle Scholar
Korinsak, S, Siangliw, M, Kotcharerk, J, Jirapong, J, Jonaliza, LS, Boonrat, J, Grienggrai, P, Nitat, S and Theerayut, T (2016) Improvement of the submergence tolerance and the brown planthopper resistance of the Thai jasmine rice cultivar KDML105 by pyramiding Sub1 and Qbph12. Field Crop Research 188, 105–112.10.1016/j.fcr.2015.10.025CrossRefGoogle Scholar
Kumar, S and Trivedi, PK (2018) Glutathione S-transferases: role in combating abiotic stresses including arsenic detoxification in plants. Frontiers in Plant Science 9, 1–9. Available at https://doi.org/10.3389/fpls.2018.00751CrossRefGoogle ScholarPubMed
Ling, J, Ming-yu, HW, Ming, C and Jian-min, W (2004) Quantitative trait loci and epistatic analysis of seed anoxia germinability in rice (Oryza sativa L.). Rice Science 11, 238–244.Google Scholar
Loque, D, Ludewig, U, Yuan, L and Von Wirén, N (2005) Tonoplast intrinsic proteins AtTIP2;1 and AtTIP2;3 facilitate NH3 transport into the vacuole. Plant Physiology 137, 671–680.10.1104/pp.104.051268CrossRefGoogle ScholarPubMed
Loreti, E, Yamaguchi, J, Alpi, A and Perata, P (2003) Gibberellins are not required for rice germination under anoxia. Plant and Soil 253, 137–143.10.1023/A:1024539011641CrossRefGoogle Scholar
Mackill, DJ, Ismail, AM, Pamplona, AM, Sanchez, DL, Carandang, JJ and Septiningsih, EM (2010) Stress tolerant rice varieties for adaptation to a changing climate. Crop Environment & Bioinformatics 7, 250–259.Google Scholar
Nawarathna, RN, Perera, ALT and Samarasinghe, WLG (2014) Screening of BC1F1 population (BG 379-2/IR 07F102//BG 379-2) of rice (Oryza sativa L.) for submergence tolerance using molecular markers. Journal of Agricultural Sciences 9, 147–153.10.4038/jas.v9i3.7437CrossRefGoogle Scholar
Neeraja, CN, Maghirang Rodriguez, R, Pamplona, A, Heuer, S, Collard, BC, Septiningsih, EM, Vergara, G, Sanchez, D, Xu, K, Ismail, AM and Mackill, DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theoretical Applied Genetics 115, 767–776.10.1007/s00122-007-0607-0CrossRefGoogle ScholarPubMed
Panda, D and Barik, J (2021) Flooding tolerance in rice: focus on mechanisms and approaches. Rice Science 28, 43–47.10.1016/j.rsci.2020.11.006CrossRefGoogle Scholar
Qi, Y, Kawano, N, Yamauchi, Y, Ling, J, Li, D and Tanaka, K (2005) Identification and cloning of a submergence-induced gene OsGGT (glycogenin glucosyltransferase) from rice (Oryza sativa L.) by suppression subtractive hybridization. Planta 221, 437–445.CrossRefGoogle ScholarPubMed
Reddy, AV, Girija Rani, M, Satyanarayana, PV, Suryanarayana, Y, Chamundeswari, N, Ravi Kumar, BNVSR, Ramana Rao, PV and Vishnuvardhan, KM (2015) Physiological and molecular response of rice genotypes for different types of flooding. Current Biotica 8, 345–350.Google Scholar
Rumanti, A, Sitaresmi, T and Nugraha, Y (2022) Rice tolerance variation to long-term stagnant flooding and germination ability under an-aerobic. IOP Conference Series: Earth Environmental Science 423, 012048.Google Scholar
Sandhya, R, Kuanar, A, Ray, S, Sethi, K, Chattopadhyay, K and Sarkar, RK (2017) Physiological basis of stagnant flooding tolerance in rice. Rice 24, 73–84.Google Scholar
Sandhya Rani, K, Kutubuddin, AM, Chattopadhyay, K, Sarkar, RK and Pravat Kumar, M (2019) Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain- filling under stagnant flooding. Scientific Reports 9, 18567.Google Scholar
Sanhez-Bermudez, M, del Pozo, JC and Pernas, M (2022) Effects of combined abiotic stresses related to climate change on root growth in crops. Frontiers in Plant Science 13, 918537.CrossRefGoogle Scholar
Sarkar, RK and Bhattacharjee, B (2011) Rice genotypes with Sub1 QTL differ in submergence tolerance, elongation ability during sub- mergence, and re-generation growth at re-emergence. Rice 5, 7.CrossRefGoogle Scholar
Septiningsih, EM, Pamplona, AM, Sanchez, DL, Neeraja, CN, Vergara, GV, Heuer, S, Ismail, AM and Mackill, DJ (2009) Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond. Annals of Botany 103, 151–160.CrossRefGoogle ScholarPubMed
Septiningsih, EM, Sanchez, DL, Singh, N, Sendon, PMD, Pamplona, AM, Heuer, S and Mackill, DJ (2012) Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theoretical and Applied Genetics 124, 867–874.CrossRefGoogle ScholarPubMed
Septiningsih, EM, Ignacio, JCI, Sendon, PMD, Sanchez, DL, Ismail, AM and Mackill, DJ (2013) QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red. Theoretical and Applied Genetics 126, 1357–1366.CrossRefGoogle ScholarPubMed
Septiningsih, EM, Hidayatun, N, Sanchez, DL, Nugraha, Y, Carandang, J, Pamplona, AM, Collard, BCY, Ismail, AM and Mackill, DJ (2014) Accelerating the development of new submergence tolerant rice varieties: the case of Ciherang-Sub1 and PSB Rc18-Sub1. Euphytica 202, 259–268.CrossRefGoogle Scholar
Singh, R, Singh, Y, Xalaxo, S, Verulkar, S, Yadav, N, Singh, S, Singh, N, Prasad, KSN, Kondayya, K, Ramana Rao, PV, Girija Rani, M, Anuradha, T, Suraynarayana, Y, Sharma, PC, Krishnamurthy, SL, Sharma, SK, Dwivedi, JL, Singh, AK, Singh, PK, Nilanjay, , Singh, NK, Kumar, R, Chetiah, SK, Ahmad, T, Rai, M, Perraju, P, Anita, P, Singh, DN, Mandal, NP, Reddy, JN, Singh, ON, Katara, JL, Marandi, B, Swain, P, Sarkar, RK, Singh, DP, Mohapatra, , Padmawathi, G, Ram, T, Kathiresan, RM, Paramsivam, K, Nadarajan, S, Thirumeni, S, Nagarajan, M, Singh, AK, Vikram, P, Kumar, A, Septiningshih, E, Singh, US, Ismail, AM, Mackill, D and Singh, NK (2016) From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network. Plant Science 242, 278–287.CrossRefGoogle ScholarPubMed
Singh, A, Carandang, J, Gonzaga, ZJC, Collard, BCY, Ismail, AM and Septiningsih, EM (2017 a) Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions. Rice 10, 15.CrossRefGoogle ScholarPubMed
Singh, A, Septiningsih, EM, Balyan, HS, Singh, NK and Rai, V (2017 b) Genetics, physiological mechanisms and breeding of flood-tolerant rice (Oryza sativa L.). Plant Cell Physiology 58, 185–197.Google ScholarPubMed
Swain, DK, Herath, S, Pathirana, A and Mittra, BN (2005) Rainfed lowland and flood prone rice: a critical review on ecology and management technology for improving the productivity in Asia. In Role of Water Sciences in Transboundary River Basin Management, Thailand.Google Scholar
Sweetaleena, S, Sandhay Rani, K and Sarkar, RK (2019) Anaerobic germination potential in rice (Oryza sativa L.): role of amylases, alcohol dehydrogenase and ethylene. Journal of Stress Physiology & Biochemistry 15, 39–52.Google Scholar
Thapa, R, Tabien, RE, Thomson, MJ and Septiningsih, EM (2022) Genetic factors underlying anaerobic germination in rice: genome-wide association study and transcriptomic analysis. The Plant Genome, e20261. Available at https://doi.org/10.1002/tpg2.20261.CrossRefGoogle ScholarPubMed
Toledo, AM, Ignacio, JCI, Casal, C, Gonzaga, ZJ, Mendioro, MS and Septiningsih, EM (2015) Development of improved Ciherang-Sub1 having tolerance to anaerobic germination conditions. Plant Breeding Biotechnology 3, 77–87.CrossRefGoogle Scholar
Toojinda, T, Siangliw, M, Tragoonrung, S and Vanavichit, A (2003) Thai Jasmine rice carrying QTLCh9 (Sub1 QTL) is submergence tolerant. Annals of Botany 91, 225–261.Google Scholar
Tyerman, SD, Niemietz, CM and Bramley, H (2002) Plant aquaporins: multifunctional water and solute channels with expanding roles. Plant Cell Environment 25, 173–194.CrossRefGoogle ScholarPubMed
Vergara, GV, Nugraha, Y, Esguerra, MQ, Mackill, DJ and Ismail, AM (2014) Variation in tolerance of rice to long-term stagnant flooding that submerges most of the shoot will aid in breeding tolerant cultivars. AoB PLANTS 6, plu055. doi: 10.1093/aobpla/plu055CrossRefGoogle ScholarPubMed
Wang, J, Li, H, Zhang, L and Meng, L (2016) User's Manual of QTL IciMapping. China: The Quantitative Genetics Group, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Mexico: Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT).Google Scholar
Xu, K, Xia, X, Fukao, T, Canlas, P, Maghirang-Rodriguez, R, Heuer, S, Ismail, AI, Bailey-Serres, J, Ronald, PC and Mackill, DJ (2006) Sub1A is an ethylene response factor-like gene that confers submergence tolerance to rice. Nature 442, 705–708.CrossRefGoogle ScholarPubMed
Yang, SY, Wu, YS, Chen, CT, Lai, MH, Yen, HM and Yang, CY (2017) Physiological and molecular responses of seedlings of an upland rice (‘Tung Lu 3’) to total submergence compared to those of a submergence-tolerant lowland rice (‘FR13A’). Rice 10, 42.CrossRefGoogle ScholarPubMed
Zheng, K, Subudhi, PK, Domingo, J, Magantay, G and Huang, N (1995) Rapid DNA isolation for marker assisted selection in rice breeding. Rice Genetics News Letter 12, 255–258.Google Scholar
Zhu, G, Chen, Y, Ella, ES and Ismail, AM (2018) Mechanisms associated with tiller suppression under stagnant flooding in rice. Journal of Agricultural Crop Science, 1–13.Google Scholar