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Liu J, Zheng W, Wang W, Yang X, Huang Y, Cui P, Ma Z, Zeng X, Zhai R, Weng X, Wu W, Zhang X. Identification of AGO2 and PLEC genes polymorphisms in Hu sheep and their relationship with body size traits. Anim Biotechnol 2024; 35:2295926. [PMID: 38149679 DOI: 10.1080/10495398.2023.2295926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The body size traits are major traits in livestock, which intuitively displays the development of the animal's bones and muscles. This study used PCR amplification, Sanger sequencing, KASPar genotyping, and quantitative real-time reverse transcription PCR (qRT-PCR) to analyze the Single-nucleotide polymorphism and expression characteristics of Argonaute RISC catalytic component 2 (AGO2) and Plectin (PLEC) genes in Hu sheep. Two intron mutations were found in Hu sheep, which were AGO2 g.51700 A > C and PLEC g.23157 C > T, respectively. Through association analysis of two mutation sites and body size traits, it was found that AGO2 g.51700 A > C mainly affects the chest and cannon circumference of Hu sheep of while PLEC g.23157 C mainly affects body height and body length. The combined genotypes of AGO2 and PLEC genes with body size traits showed SNPs at the AGO2 g.51700 A > C and PLEC g.23157 C > T loci significantly improved the body size traits of Hu sheep. In addition, the AGO2 gene has the highest expression levels in the heart, rumen, and tail fat, and the PLEC gene is highly expressed in the heart. These two loci can provide new research ideas for improving the body size traits of Hu sheep.
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Affiliation(s)
- Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Cheng X, Zhou G, Chen W, Tan L, Long Q, Cui F, Tan L, Zou G, Tan Y. Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:219. [PMID: 39254868 PMCID: PMC11387466 DOI: 10.1007/s00122-024-04729-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 08/24/2024] [Indexed: 09/11/2024]
Abstract
In the past century, there have been great achievements in identifying resistance (R) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of R genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of R genes. Here, we summarize all the R genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple R genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.
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Affiliation(s)
- Xiaoyan Cheng
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yichun, People's Republic of China
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, People's Republic of China
- College of Life Sciences and Resources and Environment, Yichun University, Yichun, People's Republic of China
| | - Guohua Zhou
- College of Life Sciences and Resources and Environment, Yichun University, Yichun, People's Republic of China
| | - Wei Chen
- Jiangxi Super-Rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, Jiangxi Academy of Agricultural Sciences, National Engineering Research Center for Rice, Nanchang, People's Republic of China
| | - Lin Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yichun, People's Republic of China
| | - Qishi Long
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yichun, People's Republic of China
| | - Fusheng Cui
- Yichun Academy of Sciences (Jiangxi Selenium-Rich Industry Research Institute), Yichun, People's Republic of China
| | - Lei Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yichun, People's Republic of China
| | - Guoxing Zou
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, People's Republic of China.
| | - Yong Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yichun, People's Republic of China.
- Jiangxi Super-Rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, Jiangxi Academy of Agricultural Sciences, National Engineering Research Center for Rice, Nanchang, People's Republic of China.
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Mohanavel V, Muthu V, Kambale R, Palaniswamy R, Seeli P, Ayyenar B, Rajagopalan V, Manickam S, Rajasekaran R, Rahman H, Nallathambi J, Swaminathan M, Chellappan G, Vellingiri G, Muthurajan R. Marker-assisted breeding accelerates the development of multiple-stress-tolerant rice genotypes adapted to wider environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1402368. [PMID: 39070911 PMCID: PMC11272538 DOI: 10.3389/fpls.2024.1402368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/03/2024] [Indexed: 07/30/2024]
Abstract
Introduction Rice, one of the major staple food crops is frequently affected by various biotic/abiotic stresses including drought, salinity, submergence, heat, Bacterial leaf blight, Brown plant hopper, Gall midge, Stem borer, Leaf folder etc. Sustained increase of yield growth is highly necessary to meet the projected demand in rice production during the year 2050. Hence, development of high yielding and multiple stress tolerant rice varieties adapted to wider environments will serve the need. Methods A systematic MAB approach was followed to pyramid eight major QTLs/genes controlling tolerance to major abiotic/biotic stresses viz., drought (qDTY1.1 and qDTY2.1), salinity (Saltol), submergence (Sub1), bacterial leaf blight (xa13 and Xa21), blast (Pi9) and gall midge (Gm4) in the genetic background of an elite rice culture CBMAS 14065 possessing high yield and desirable grain quality traits. Two advanced backcross derivatives of CBMAS 14065 possessing different combinations of target QTLs namely #27-1-39 (qDTY1.1+qDTY2.1+Sub1+xa13+Xa21+Gm4+Pi9) and #29-2-2 (qDTY1.1+qDTY2.1+Saltol+Xa21+Gm4+Pi9) were inter-mated. Results Inter-mated F1 progenies harboring all the eight target QTLs/genes were identified through foreground selection. Genotyping of the inter-mated F4 population identified 14 progenies possessing all eight target QTLs/genes under homozygous conditions. All the fourteen progenies were forwarded up to F8 generation and evaluated for their yield and tolerance to dehydration, salinity, submergence, blast and bacterial leaf blight. All the 14 progenies exhibited enhanced tolerance to dehydration and salinity stresses by registering lesser reduction in their chlorophyll content, relative water content, root length, root biomass etc., against their recurrent parent Improved White Ponni/CBMAS 14065. All the 14 progenies harboring Sub1 loci from FR13A exhibited enhanced survival (90 - 95%) under 2 weeks of submergence /flooding when compared to their recurrent parent CBMAS 14065 which showed 100% susceptibility The inter-mated population showed a enhanced level of resistance to bacterial leaf blight (Score = 0 to 2) against blast (Score - 0) whereas the susceptible check CO 39 and the recurrent parent CBMAS 14065 recorded high level of susceptibility (Score = 7 to 9). Conclusion or discussion Our study demonstrated the accelerated development of multiple stress tolerant rice genotypes through marker assisted pyramiding of target QTLs/genes using tightly linked markers. These multiple stress tolerant rice lines will serve as excellent genetic stocks for field testing/variety release and also as parental lines in future breeding programs for developing climate resilient super rice varieties.
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Affiliation(s)
- Vignesh Mohanavel
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Valarmathi Muthu
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Rohit Kambale
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Rakshana Palaniswamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Prisca Seeli
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Bharathi Ayyenar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Veeraranjani Rajagopalan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sudha Manickam
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Hifzur Rahman
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
- International Centre for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Jagadeeshselvam Nallathambi
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Manonmani Swaminathan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Gopalakrishnan Chellappan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Tiwari K, Tiwari S, Kumar N, Sinha S, Krishnamurthy SL, Singh R, Kalia S, Singh NK, Rai V. QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued. PLANTS (BASEL, SWITZERLAND) 2024; 13:1099. [PMID: 38674508 PMCID: PMC11054697 DOI: 10.3390/plants13081099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 04/28/2024]
Abstract
Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.
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Affiliation(s)
- Keshav Tiwari
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sushma Tiwari
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Nivesh Kumar
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Shikha Sinha
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | | | - Renu Singh
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, New Delhi 110003, India
| | - Nagendra Kumar Singh
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Vandna Rai
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
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Singh P, Sundaram KT, Vinukonda VP, Venkateshwarlu C, Paul PJ, Pahi B, Gurjar A, Singh UM, Kalia S, Kumar A, Singh VK, Sinha P. Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties. Commun Biol 2024; 7:89. [PMID: 38216712 PMCID: PMC10786901 DOI: 10.1038/s42003-024-05769-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.
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Affiliation(s)
- Preeti Singh
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | | | | | - Pronob J Paul
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Bandana Pahi
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Anoop Gurjar
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Sanjay Kalia
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, India
| | - Arvind Kumar
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India.
| | - Pallavi Sinha
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India.
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Varanasi YVP, Isetty SR, Revadi P, Balakrishnan D, Hajira S, Prasad MS, Laha GS, Perraju P, Singh UM, Singh VK, Kumar A, Sundaram RM, Badri J. Molecular and Morphological Characterization of Introgression Lines with Resistance to Bacterial Leaf Blight and Blast in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3012. [PMID: 37631223 PMCID: PMC10458744 DOI: 10.3390/plants12163012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023]
Abstract
The present study evaluates marker assisted forward breeding (MAFB)-derived disease resistant introgression lines (ILs) which do not have the targeted resistance genes for bacterial blight (xa5 + xa13 + Xa21) and blast (Pi2 + Pi9 + Pi54). The ILs were derived in the background of two elite rice cultivars, Krishna Hamsa [Recurrent Parent 1 (RP1)] and WGL 14 (RP2), involving multi-parent inter-crossing. Molecular characterization with gene specific markers for seven reported resistance genes each for bacterial blight (Xa33, Xa38, xa23, Xa4, xa8, Xa27 and Xa41) and blast (Pi1, Pi20, Pi38, Pib, Pitp, Pizt and Pi40) revealed the presence of xa8 and Xa38, in addition to the targeted xa5, xa13 and Xa21 for bacterial blight resistance and Pi1, Pi38, Pi40, Pi20, Pib and Pipt, in addition to the targeted Pi9 and Pi54, for blast resistance in various combinations. A maximum of nine resistance genes xa5 + Xa21 + Pi54 + xa8 + Pipt + Pi38 + Pi1 + Pi20 + Pib was observed in RP1-IL 19030 followed by eight genes xa5 + xa13 + Xa21 + xa8 + Pi9 + Pipt + Pi1 + Pi20 in two RP2-ILs, 19344 and 19347. ANOVA revealed the presence of significant variability for all the yield traits except "days to 50% flowering" (DFF). Box plots depicted the seasonal differences in the phenotypic expression of the yield traits. There was significant positive association of grain yield with days to flowering, tiller number and panicle number. Thousand grain weight is also significantly and positively correlated with grain yield. On the contrary, grain yield showed a significantly negative association with plant height. Multi-parent selective inter-crossing in the present study not only led to the development of high yielding disease resistant ILs but also enhanced recovery of the recurrent parent via selection for essential morphological features. More than 90.0% genetic similarity in the ILs based on SNP-based background selection demonstrated the success of multi-parent selective intercrossing in the development of disease resistant NILs.
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Affiliation(s)
- Yasaswini Vishnu Priya Varanasi
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
- Jawaharlal Nehru Krishi Vishwa Vidyalaya, Rewa 486001, India
| | | | - Padmashree Revadi
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | - Divya Balakrishnan
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | - Shaik Hajira
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | | | - Gouri Shankar Laha
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | - Puvvada Perraju
- Jawaharlal Nehru Krishi Vishwa Vidyalaya, Rewa 486001, India
| | - Uma Maheshwar Singh
- International Rice Research Institute South Asia Regional Centre (ISARC), Varanasi 221006, India
| | - Vikas Kumar Singh
- International Rice Research Institute South Asia Hub (IRRISAH), Hyderabad 221106, India;
| | - Arvind Kumar
- International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | | | - Jyothi Badri
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
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Saleem A, Roldán-Ruiz I, Aper J, Muylle H. Genetic control of tolerance to drought stress in soybean. BMC PLANT BIOLOGY 2022; 22:615. [PMID: 36575367 PMCID: PMC9795773 DOI: 10.1186/s12870-022-03996-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Drought stress limits the production of soybean [Glycine max (L.) Merr.], which is the most grown high-value legume crop worldwide. Breeding for drought tolerance is a difficult endeavor and understanding the genetic basis of drought tolerance in soybean is therefore crucial for harnessing the genomic regions involved in the tolerance mechanisms. A genome-wide association study (GWAS) analysis was applied in a soybean germplasm collection (the EUCLEG collection) of 359 accessions relevant for breeding in Europe, to identify genomic regions and candidate genes involved in the response to short duration and long duration drought stress (SDS and LDS respectively) in soybean. RESULTS The phenotypic response to drought was stronger in the long duration drought (LDS) than in the short duration drought (SDS) experiment. Over the four traits considered (canopy wilting, leaf senescence, maximum absolute growth rate and maximum plant height) the variation was in the range of 8.4-25.2% in the SDS, and 14.7-29.7% in the LDS experiments. The GWAS analysis identified a total of 17 and 22 significant marker-trait associations for four traits in the SDS and LDS experiments, respectively. In the genomic regions delimited by these markers we identified a total of 12 and 16 genes with putative functions that are of particular relevance for drought stress responses including stomatal movement, root formation, photosynthesis, ABA signaling, cellular protection and cellular repair mechanisms. Some of these genomic regions co-localized with previously known QTLs for drought tolerance traits including water use efficiency, chlorophyll content and photosynthesis. CONCLUSION Our results indicate that the mechanism of slow wilting in the SDS might be associated with the characteristics of the root system, whereas in the LDS, slow wilting could be due to low stomatal conductance and transpiration rates enabling a high WUE. Drought-induced leaf senescence was found to be associated to ABA and ROS responses. The QTLs related to WUE contributed to growth rate and canopy height maintenance under drought stress. Co-localization of several previously known QTLs for multiple agronomic traits with the SNPs identified in this study, highlights the importance of the identified genomic regions for the improvement of agronomic performance in addition to drought tolerance in the EUCLEG collection.
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Affiliation(s)
- Aamir Saleem
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Jonas Aper
- Protealis, Technologiepark-Zwijnaarde, Ghent, Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium.
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Sahu PK, Sao R, Choudhary DK, Thada A, Kumar V, Mondal S, Das BK, Jankuloski L, Sharma D. Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease. PLANTS 2022; 11:plants11182386. [PMID: 36145787 PMCID: PMC9504543 DOI: 10.3390/plants11182386] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 01/02/2023]
Abstract
Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | | | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
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9
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Screening methods for cereal grains with different starch components: A mini review. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Multiparent-Derived, Marker-Assisted Introgression Lines of the Elite Indian Rice Cultivar, ‘Krishna Hamsa’ Show Resistance against Bacterial Blight and Blast and Tolerance to Drought. PLANTS 2022; 11:plants11050622. [PMID: 35270092 PMCID: PMC8912774 DOI: 10.3390/plants11050622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
Major biotic stresses viz., bacterial blight (BB) and blast and brown plant hopper (BPH) coupled with abiotic stresses like drought stress, significantly affect rice yields. To address this, marker-assisted intercross (IC) breeding involving multiple donors was used to combine three BB resistance genes—xa5, xa13 and Xa21, two blast resistance genes—Pi9 and Pi54, two BPH resistance genes—Bph20 and Bph21, and four drought tolerant quantitative trait loci (QTL)—qDTY1.1, qDTY2.1, qDTY3.1 and qDTY12.1—in the genetic background of the elite Indian rice cultivar ‘Krishna Hamsa’. Three cycles of selective intercrossing followed by selfing coupled with foreground selection and phenotyping for the target traits resulted in the development of 196 introgression lines (ILs) with a myriad of gene/QTL combinations. Based on the phenotypic reaction, the ILs were classified into seven phenotypic classes of resistance/tolerance to the following: (1) BB, blast and drought—5 ILs; (2) BB and blast—10 ILs; (3) BB and drought—9 ILs; (4) blast and drought—42 ILs; (5) BB—3 ILs; (6) blast—84 ILs; and (7) drought—43 ILs; none of the ILs were resistant to BPH. Positive phenotypic response (resistance) was observed to both BB and blast in 2 ILs, BB in 9 ILs and blast in 64 ILs despite the absence of corresponding R genes. Inheritance of resistance to BB and/or blast in such ILs could be due to the unknown genes from other parents used in the breeding scheme. Negative phenotypic response (susceptibility) was observed in 67 ILs possessing BB-R genes, 9 ILs with blast-R genes and 9 ILs harboring QTLs for drought tolerance. Complex genic interactions and recombination events due to the involvement of multiple donors explain susceptibility in some of the marker positive ILs. The present investigation successfully demonstrates the possibility of rapid development of multiple stress-tolerant/resistant ILs in the elite cultivar background involving multiple donors through selective intercrossing and stringent phenotyping. The 196 ILs in seven phenotypic classes with myriad of gene/QTL combinations will serve as a useful genetic resource in combining multiple biotic and abiotic stress resistance in future breeding programs.
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