1
|
Prahalada GD, Marathi B, Vinarao R, Kim SR, Diocton R, Ramos J, Jena KK. QTL Mapping of a Novel Genomic Region Associated with High Out-Crossing Rate Derived from Oryza longistaminata and Development of New CMS Lines in Rice, O. sativa L. Rice (N Y) 2021; 14:80. [PMID: 34529158 PMCID: PMC8446144 DOI: 10.1186/s12284-021-00521-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/30/2021] [Indexed: 05/27/2023]
Abstract
High seed cost due to poor seed yield severely limits the adoption of hybrid rice by farmers. Increasing the out-crossing rate is one of the key strategies to increase hybrid seed production. Out-crossing rate is highly influenced by the size of female floral traits, which capture pollen grains from male donor plants. In the current study, we identified 14 QTLs derived from the perennial wild rice Oryza longistaminata by composite interval mapping for five key floral traits: stigma length (five), style length (three), stigma breadth (two), stigma area (one), and pistil length (three). QTL analysis and correlation studies revealed that these stigma traits were positively correlated and pleiotropic to the stigma length trait. We selected the major-effect QTL qSTGL8.0 conferring long stigma phenotype for further fine mapping and marker-assisted selection. The qSTGL8.0 (~ 3.9 Mb) was fine mapped using newly developed internal markers and was narrowed down to ~ 2.9 Mb size (RM7356-RM256 markers). Further, the flanking markers were validated in a segregating population and in progenies from different genetic backgrounds. The markers PA08-03 and PA08-18 showed the highest co-segregation with the stigma traits. The qSTGL8.0 was introgressed into two cytoplasmic male sterile (CMS) lines, IR58025A and IR68897A, by foreground, background, and trait selection approaches. The qSTGL8.0 introgression lines in CMS backgrounds showed a significantly higher seed setting rate (2.5-3.0-fold) than the original CMS lines in test crosses with their corresponding maintainer lines. The newly identified QTLs especially qSTGL8.0, will be quite useful for increasing out-crossing rate and this will contribute to increase seed production and decrease seed cost.
Collapse
Affiliation(s)
- G D Prahalada
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Balram Marathi
- PJ Telangana State Agricultural University, Hyderabad, Telangana, 500030, India
| | - Ricky Vinarao
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Reynaldo Diocton
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Joie Ramos
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
| |
Collapse
|
2
|
Mahender A, Ali J, Prahalada GD, Sevilla MAL, Balachiranjeevi CH, Md J, Maqsood U, Li Z. Genetic dissection of developmental responses of agro-morphological traits under different doses of nutrient fertilizers using high-density SNP markers. PLoS One 2019; 14:e0220066. [PMID: 31335882 PMCID: PMC6650078 DOI: 10.1371/journal.pone.0220066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The production and productivity of rice (Oryza sativa L.) are primarily influenced by the application of the critical nutrients nitrogen (N), phosphorus (P), and potassium (K). However, excessive application of these fertilizers is detrimental to the environment and increases the cost of production. Hence, there is a need to develop varieties that simultaneously increase yields under both optimal and suboptimal rates of fertilizer application by maximizing nutrient use efficiency (NuUE). To unravel the hidden genetic variation and understand the molecular and physiological mechanisms of NuUE, three different mapping populations (MPs; BC1F5) derived from three donors (Haoannong, Cheng-Hui 448, and Zhong 413) and recipient Weed Tolerant Rice 1 were developed. A total of three favorable agronomic traits (FATs) were considered as the measure of NuUE. Analysis of variance and descriptive statistics indicated the existence of genetic variation for NuUE and quantitative inheritance of FATs. The genotypic data from single-nucleotide polymorphism (SNP) markers from Tunable Genotyping-By-Sequencing (tGBS) and phenotypic values were used for locating the genomic regions conferring NuUE. A total of 19 quantitative trait loci (QTLs) were detected, out of which 11 QTLs were putative on eight chromosomes, which individually explained 17.02% to 34.85% of the phenotypic variation. Notably, qLC-II_1 and qLC-II_11 detected at zero fertilizer application showed higher performance for LC under zero percentage of NPK fertilizer. The remarkable findings of the present study are that the detected QTLs were associated in building tolerance to low/no nutrient application and six candidate genes on chromosomes 2 and 5 within these putative QTLs were found associated with low nutrient tolerance and related to several physiological and metabolic pathways involved in abiotic stress tolerance. The identified superior introgressed lines (ILs) and trait-associated genetic regions can be effectively used in marker-assisted selection (MAS) for NuUE breeding programs.
Collapse
Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
- * E-mail:
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Ma. Anna Lynn Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - C. H. Balachiranjeevi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jamaloddin Md
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan
| | - Zhikang Li
- Chinese Academy of Agricultural Sciences, Haidian District, P.R. China
| |
Collapse
|
3
|
Balachiranjeevi CH, Prahalada GD, Mahender A, Jamaloddin M, Sevilla MAL, Marfori-Nazarea CM, Vinarao R, Sushanto U, Baehaki SE, Li ZK, Ali J. Identification of a novel locus, BPH38(t), conferring resistance to brown planthopper ( Nilaparvata lugens Stal.) using early backcross population in rice ( Oryza sativa L.). Euphytica 2019; 215:185. [PMID: 31885402 PMCID: PMC6913135 DOI: 10.1007/s10681-019-2506-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/26/2019] [Indexed: 05/05/2023]
Abstract
Rice is the most important staple food crop, and it feeds more than half of the world population. Brown planthopper (BPH) is a major insect pest of rice that causes 20-80% yield loss through direct and indirect damage. The identification and use of BPH resistance genes can efficiently manage BPH. A molecular marker-based genetic analysis of BPH resistance was carried out using 101 BC1F5 mapping population derived from a cross between a BPH-resistant indica variety Khazar and an elite BPH-susceptible line Huang-Huan-Zhan. The genetic analysis indicated the existence of Mendelian segregation for BPH resistance. A total of 702 high-quality polymorphic single nucleotide polymorphism (SNP) markers, genotypic data, and precisely estimated BPH scores were used for molecular mapping, which resulted in the identification of the BPH38(t) locus on the long arm of chromosome 1 between SNP markers 693,369 and id 10,112,165 of 496.2 kb in size with LOD of 20.53 and phenotypic variation explained of 35.91%. A total of 71 candidate genes were predicted in the detected locus. Among these candidate genes, LOC_Os01g37260 was found to belong to the FBXL class of F-box protein possessing the LRR domain, which is reported to be involved in biotic stress resistance. Furthermore, background analysis and phenotypic selection resulted in the identification of introgression lines (ILs) possessing at least 90% recurrent parent genome recovery and showing superior performance for several agro-morphological traits. The BPH resistance locus and ILs identified in the present study will be useful in marker-assisted BPH resistance breeding programs.
Collapse
Affiliation(s)
- C. H. Balachiranjeevi
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - A. Mahender
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Md. Jamaloddin
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - M. A. L. Sevilla
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - C. M. Marfori-Nazarea
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - R. Vinarao
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - U. Sushanto
- Indonesian Center for Rice Research, Sukamandi, Indonesia
| | - S. E. Baehaki
- Indonesian Center for Rice Research, Sukamandi, Indonesia
| | - Z. K. Li
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - J. Ali
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| |
Collapse
|
4
|
Kim SR, Torollo G, Yoon MR, Kwak J, Lee CK, Prahalada GD, Choi IR, Yeo US, Jeong OY, Jena KK, Lee JS. Loss-of-Function Alleles of Heading date 1 ( Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region. Front Plant Sci 2018; 9:1827. [PMID: 30619400 PMCID: PMC6295564 DOI: 10.3389/fpls.2018.01827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/26/2018] [Indexed: 05/11/2023]
Abstract
Adaptation of temperate japonica rice varieties to tropical regions is impeded by extremely early flowering probably due to photoperiod change from long to short. However, constant breeding efforts led to development of temperate japonica varieties adapted to tropical/subtropical regions, but the genetic factor underlying this is still elusive. We analyzed the 45 diverse rice accessions and 12 tropical-adapted temperate japonica lines for the allele types of seven major flowering genes Hd1, OsPPR37, DTH8, Ghd7, Ehd1, RFT1, and Hd3a and flowering time under three different field conditions in temperate and tropical locations. The accessions originated from the tropical/subtropical regions preferred the non-functional alleles of Hd1 and not other flowering genes. The genetic effect analysis of each gene showed that only the functional Hd1 caused early flowering in the tropical location. All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate japonica varieties. These results indicate that the functional Hd1 alleles of temperate japonica varieties induced extremely early flowering in the tropics and the non-functional hd1 alleles brought about the adaptation of temperate japonica rice to tropical regions.
Collapse
Affiliation(s)
- Sung-Ryul Kim
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Gideon Torollo
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Mi-Ra Yoon
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - Jieun Kwak
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - Choon-Ki Lee
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Il-Ryong Choi
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Un-Sang Yeo
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - O-Young Jeong
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - Kshirod K. Jena
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Jeom-Sig Lee
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| |
Collapse
|
5
|
Hechanova SL, Prusty MR, Kim SR, Ballesfin L, Ramos J, Prahalada GD, Jena KK. Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application. Theor Appl Genet 2018; 131:2197-2211. [PMID: 30032316 DOI: 10.1007/s00122-018-3147-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/14/2018] [Indexed: 05/23/2023]
Abstract
Key message Development of MAALs and disomic introgression lines derived from the cross between O. sativa and O. rhizomatis to exploit and utilize the valuable traits for rice improvement. The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F1, and the F1 plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC1F1 and 73 BC2F1 plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F1, BC1F1, BC2F2, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars.
Collapse
Affiliation(s)
- Sherry Lou Hechanova
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Manas R Prusty
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - LaRue Ballesfin
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Joie Ramos
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - G D Prahalada
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| |
Collapse
|
6
|
Jena KK, Hechanova SL, Verdeprado H, Prahalada GD, Kim SR. Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis. Theor Appl Genet 2017; 130:2345-2360. [PMID: 28795219 DOI: 10.1007/s00122-017-2963-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/01/2017] [Indexed: 05/21/2023]
Abstract
A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BC3F5) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.
Collapse
Affiliation(s)
- Kshirod K Jena
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| | - Sherry Lou Hechanova
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Holden Verdeprado
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - G D Prahalada
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| |
Collapse
|
7
|
Prahalada GD, Shivakumar N, Lohithaswa HC, Sidde Gowda DK, Ramkumar G, Kim SR, Ramachandra C, Hittalmani S, Mohapatra T, Jena KK. Identification and fine mapping of a new gene, BPH31 conferring resistance to brown planthopper biotype 4 of India to improve rice, Oryza sativa L. Rice (N Y) 2017; 10:41. [PMID: 28861736 PMCID: PMC5578944 DOI: 10.1186/s12284-017-0178-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/11/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is the staple food for more than 3.5 billion people, mainly in Asia. Brown planthopper (BPH) is one of the most destructive insect pests of rice that limits rice production. Host-plant resistance is one of the most efficient ways to overcome BPH damage to the rice crop. RESULTS BPH bioassay studies from 2009 to 2015 conducted in India and at the International Rice Research Institute (IRRI), Philippines, revealed that the cultivar CR2711-76 developed at the National Rice Research Institute (NRRI), Cuttack, India, showed stable and broad-spectrum resistance to several BPH populations of the Philippines and BPH biotype 4 of India. Genetic analysis and fine mapping confirmed the presence of a single dominant gene, BPH31, in CR2711-76 conferring BPH resistance. The BPH31 gene was located on the long arm of chromosome 3 within an interval of 475 kb between the markers PA26 and RM2334. Bioassay analysis of the BPH31 gene in CR2711-76 was carried out against BPH populations of the Philippines. The results from bioassay revealed that CR2711-76 possesses three different mechanisms of resistance: antibiosis, antixenosis, and tolerance. The effectiveness of flanking markers was tested in a segregating population and the InDel type markers PA26 and RM2334 showed high co-segregation with the resistance phenotype. Foreground and background analysis by tightly linked markers as well as using the Infinium 6 K SNP chip respectively were applied for transferring the BPH31 gene into an indica variety, Jaya. The improved BPH31-derived Jaya lines showed strong resistance to BPH biotypes of India and the Philippines. CONCLUSION The new BPH31 gene can be used in BPH resistance breeding programs on the Indian subcontinent. The tightly linked DNA markers identified in the study have proved their effectiveness and can be utilized in BPH resistance breeding in rice.
Collapse
Affiliation(s)
- G. D. Prahalada
- Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - N. Shivakumar
- Zonal Agricultural Research Station, VC Farm, Mandya, Karnataka India
| | | | | | - G. Ramkumar
- Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - C. Ramachandra
- Zonal Agricultural Research Station, VC Farm, Mandya, Karnataka India
| | | | | | - Kshirod K. Jena
- Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| |
Collapse
|