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Bharamappanavara M, Siddaiah AM, Ponnuvel S, Ramappa L, Patil B, Appaiah M, Maganti SM, Sundaram RM, Shankarappa SK, Tuti MD, Banugu S, Parmar B, Rathod S, Barbadikar KM, Kota S, Subbarao LV, Mondal TK, Channappa G. Mapping QTL hotspots associated with weed competitive traits in backcross population derived from Oryza sativa L. and O. glaberrima Steud. Sci Rep 2020; 10:22103. [PMID: 33328509 PMCID: PMC7744529 DOI: 10.1038/s41598-020-78675-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
To improve grain yield under direct seeded and aerobic conditions, weed competitive ability of a rice genotype is a key desirable trait. Hence, understanding and dissecting weed competitive associated traits at both morphological and molecular level is important in developing weed competitive varieties. In the present investigation, the QTLs associated with weed competitive traits were identified in BC1F2:3 population derived from weed competitive accession of O. glaberrima (IRGC105187) and O. sativa cultivar IR64. The mapping population consisting of 144 segregating lines were phenotyped for 33 weed competitive associated traits under direct seeded condition. Genetic analysis of weed competitive traits carried out in BC1F2:3 population showed significant variation for the weed competitive traits and predominance of additive gene action. The population was genotyped with 81 genome wide SSR markers and a linkage map covering 1423 cM was constructed. Composite interval mapping analysis identified 72 QTLs linked to 33 weed competitive traits which were spread on the 11 chromosomes. Among 72 QTLs, 59 were found to be major QTLs (> 10% PVE). Of the 59 major QTLs, 38 had favourable allele contributed from the O. glaberrima parent. We also observed nine QTL hotspots for weed competitive traits (qWCA2a, qWCA2b, qWCA2c, qWCA3, qWCA5, qWCA7, qWCA8, qWCA9, and qWCA10) wherein several QTLs co-localised. Our study demonstrates O. glaberrima species as potential source for improvement for weed competitive traits in rice and identified QTLs hotspots associated with weed competitive traits.
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Affiliation(s)
| | | | | | - Lokesha Ramappa
- University of Agricultural Science, Raichur, Karnataka, 584104, India
| | - Basavaraj Patil
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Manoj Appaiah
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | | | | | - Mangal Deep Tuti
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Sreedevi Banugu
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Brajendra Parmar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Santosha Rathod
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
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Wang M, Yang J, Wan J, Tao D, Zhou J, Yu D, Xu P. A hybrid sterile locus leads to the linkage drag of interspecific hybrid progenies. PLANT DIVERSITY 2020; 42:370-375. [PMID: 33134621 PMCID: PMC7584790 DOI: 10.1016/j.pld.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 06/02/2023]
Abstract
Interspecific hybridization plays an important role in rice breeding by broadening access to desirable traits such as disease resistance and improving yields. However, interspecific hybridization is often hindered by hybrid sterility, linkage drag, and distorted segregation. To mine for favorable genes from Oryza glaberrima, we cultivated a series of BC4 introgression lines (ILs) of O. glaberrima in the japonica rice variety background (Dianjingyou 1) in which the IL-2769 (BC4F10) showed longer sterile lemmas, wider grains and spreading panicles compared with its receptor parent, suggesting that linkage drag may have occurred. Based on the BC5F2 population, a hybrid sterility locus, S20, a long sterile lemma locus, G1-g, and a new grain width quantitative trait locus (QTL), qGW7, were mapped in the linkage region about 15 centimorgan (cM) from the end of the short arm of chromosome 7. The hybrid sterility locus S20 from O. glaberrima eliminated male gametes of Oryza sativa, and male gametes carrying the alleles of O. sativa in the heterozygotes were aborted completely. In addition, the homozygotes presented a genotype of O. glaberrima, and homozygous O. sativa were not produced. Surprisingly, the linked traits G1-g and qGW7 showed similar segregation distortion. These results indicate that S20 was responsible for the linkage drag. As a large number of detected hybrid sterility loci are widely distributed on rice chromosomes, we suggest that hybrid sterility loci are the critical factors for the linkage drag in interspecific and subspecific hybridization of rice.
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Affiliation(s)
- Mianmian Wang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Yang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinpeng Wan
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, Yunnan, China
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, Yunnan, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Peng Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
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Li J, Zhou J, Zhang Y, Yang Y, Pu Q, Tao D. New Insights Into the Nature of Interspecific Hybrid Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:555572. [PMID: 33072142 PMCID: PMC7538986 DOI: 10.3389/fpls.2020.555572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/01/2020] [Indexed: 06/01/2023]
Abstract
Interspecific and intraspecific hybrid sterility is a typical and common phenomenon of postzygotic reproductive barrier in rice. This is an indicator of speciation involved in the formation of new species or subspecies, and it significantly hampers the utilization of favorable genes from distant parents for rice improvement. The Oryza genus includes eight species with the same AA genome and is a model plant for studying the nature of hybrid sterility and its relationship with speciation. Hybrid sterility in rice is mostly controlled by nuclear genes, with more than 50 sterility loci genetically identified to date, of which 10 hybrid sterility loci or pairs were cloned and characterized at the molecular level. Comparing the mapping results for all sterility loci reported indicated that some of these loci from different species should be allelic to each other. Further research revealed that interactions between the multiple alleles at the hybrid sterility locus caused various genetic effect. One hypothesis for this important phenomenon is that the hybrid sterility loci are orthologous loci, which existed in ancient ancestors of rice. When one or more ancestors drifted to different continents, genetic divergence occurred because of adaptation, selection, and isolation among them such that various alleles from orthologous loci emerged over evolutionary time; hence, interspecific hybrid sterility would be mainly controlled by a few orthologous loci with different alleles. This hypothesis was tested and supported by the molecular characterization of hybrid sterility loci from S1, S5, Sa, qHMS7, and S27. From this, we may further deduce that both allelic and non-allelic interactions among different loci are the major genetic basis for the interspecific hybrid sterility between O. sativa and its AA genome relatives, and the same is true for intraspecific hybrid sterility in O. sativa. Therefore, it is necessary to raise the near-isogenic lines with various alleles/haplotypes and pyramided different alleles/haplotypes from sterile loci in the same genetic background aiming to study allelic and non-allelic interaction among different hybrid sterility loci in the AA genome species. Furthermore, the pyramiding lines ought to be used as bridge parents to overcome hybrid sterility for rice breeding purposes.
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Neelam K, Mahajan R, Gupta V, Bhatia D, Gill BK, Komal R, Lore JS, Mangat GS, Singh K. High-resolution genetic mapping of a novel bacterial blight resistance gene xa-45(t) identified from Oryza glaberrima and transferred to Oryza sativa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:689-705. [PMID: 31811315 DOI: 10.1007/s00122-019-03501-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/30/2019] [Indexed: 05/07/2023]
Abstract
A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F2 and F2:3 populations for inheritance and mapping studies. The inheritance studies revealed the presence of single recessive locus controlling resistance to the Xanthomonas pathotype seven. A high-density linkage map was constructed using double-digest restriction-associated DNA sequencing of 96 F2 populations along with the parents. The QTL mapping identified a major locus on the long arm of rice chromosome 8 with a LOD score of 33.22 between the SNP markers C8.26737175 and C8.26818765. The peak marker, C8.26810477, explains 49.8% of the total phenotypic variance and was positioned at 202.90 cM on the linkage map. This major locus spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. A co-segregating STS marker was developed from the LOC_Os08g42410 for efficient transfer of this novel gene to elite cultivars.
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Affiliation(s)
- Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Ritu Mahajan
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Vikas Gupta
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Dharminder Bhatia
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Baljeet Kaur Gill
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Ratika Komal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jagjeet Singh Lore
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gurjit Singh Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110073, India.
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