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Attamah P, Kusi F, Kena AW, Awuku FJ, Lamini S, Mensah G, Zackaria M, Owusu EY, Akromah R. Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing. Heliyon 2024; 10:e31976. [PMID: 38868054 PMCID: PMC11167344 DOI: 10.1016/j.heliyon.2024.e31976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers' preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.
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Affiliation(s)
- Patrick Attamah
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Francis Kusi
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Alexander Wireko Kena
- Kwame Nkrumah University of Science and Technology, Department of Crop and Soil Sciences, Kumasi, Ghana
| | - Frederick J. Awuku
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Salim Lamini
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Gloria Mensah
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Mukhtaru Zackaria
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Emmanuel Yaw Owusu
- CSIR-Savanna Agricultural Research Institute, P.O. Box TL 52, Tamale, Ghana
| | - Richard Akromah
- Kwame Nkrumah University of Science and Technology, Department of Crop and Soil Sciences, Kumasi, Ghana
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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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Liu H, Rao D, Guo T, Gangurde SS, Hong Y, Chen M, Huang Z, Jiang Y, Xu Z, Chen Z. Whole Genome Sequencing and Morphological Trait-Based Evaluation of UPOV Option 2 for DUS Testing in Rice. Front Genet 2022; 13:945015. [PMID: 36092943 PMCID: PMC9458885 DOI: 10.3389/fgene.2022.945015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
To evaluate the application potential of high-density SNPs in rice distinctness, uniformity, and stability (DUS) testing, we screened 37,929 SNP loci distributed on 12 rice chromosomes based on whole-genome resequencing of 122 rice accessions. These SNP loci were used to analyze the DUS testing of rice varieties based on the correlation between the molecular and phenotypic distances of varieties according to UPOV option 2. The results showed that statistical algorithms and the number of phenotypic traits and SNP loci all affected the correlation between the molecular and phenotypic distances of rice varieties. Relative to the other nine algorithms, the Jaccard similarity algorithm had the highest correlation of 0.6587. Both the number of SNPs and the number of phenotypes had a ceiling effect on the correlation between the molecular and phenotypic distances of varieties, and the ceiling effect of the number of SNP loci was more obvious. To overcome the correlation bottleneck, we used the genome-wide prediction method to predict 30 phenotypic traits and found that the prediction accuracy of some traits, such as the basal sheath anthocyanin color, glume length, and intensity of the green color of the leaf blade, was very low. In combination with group comparison analysis, we found that the key to overcoming the ceiling effect of correlation was to improve the resolution of traits with low predictive values. In addition, we also performed distinctness testing on rice varieties by using the molecular distance and phenotypic distance, and we found that there were large differences between the two methods, indicating that UPOV option 2 alone cannot replace the traditional phenotypic DUS testing. However, genotype and phenotype analysis together can increase the efficiency of DUS testing.
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Affiliation(s)
- Hong Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dehua Rao
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Sunil S. Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Mengqiang Chen
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhanquan Huang
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuan Jiang
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhenjiang Xu
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- *Correspondence: Zhenjiang Xu, ; Zhiqiang Chen,
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- *Correspondence: Zhenjiang Xu, ; Zhiqiang Chen,
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Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions. J Fungi (Basel) 2022; 8:jof8060584. [PMID: 35736067 PMCID: PMC9224618 DOI: 10.3390/jof8060584] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.
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Liu Y, Zhang F, Luo X, Kong D, Zhang A, Wang F, Pan Z, Wang J, Bi J, Luo L, Liu G, Yu X. Molecular Breeding of a Novel PTGMS Line of WDR for Broad-Spectrum Resistance to Blast Using Pi9, Pi5, and Pi54 Genes. RICE (NEW YORK, N.Y.) 2021; 14:96. [PMID: 34825287 PMCID: PMC8617131 DOI: 10.1186/s12284-021-00537-1] [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: 03/30/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The two-line method based on the photoperiod and thermo-sensitive genic male sterile (PTGMS) lines is more cost-effective, simple, and efficient than the three-line system based on cytoplasmic male-sterility. Blast and drought are the most prevalent biotic and abiotic stress factors hampering rice production. Molecular techniques demonstrate higher efficacy in the pyramiding of disease resistance genes, providing green performance under the background of water-saving and drought-resistance rice. RESULTS This study employed molecular marker-assisted selection, conventional hybridization, and high-intensity stress screening to integrate three broad-spectrum blast resistance genes Pi9, Pi5, and Pi54 into Huhan 1S. Subsequently, a novel water-saving and drought-resistance rice (WDR) PTGMS line Huhan 74S was developed. The drought resistance of the new PTGMS line Huhan 74S was comparable to that of Huhan 1S. Pathogenicity assays involving the inoculation of 14 blast prevalent isolates in the glasshouse showed that the blast resistance frequency of Huhan 74S was 85.7%. Further evaluation under natural blast epidemic field conditions showed that Huhan 74S and its hybrids were resistant to leaf and neck blast. The critical temperature point of fertility-sterility alteration of Huhan 74S was 23 °C daily mean temperature. The complete male sterility under natural growth conditions in 2017 at Shanghai lasted for 67 days. Also, both the agronomic and grain quality traits met the requirement for two-line hybrid rice production. CONCLUSION These results indicate that the newly bred PTGMS line Huhan 74S can be used to breed high-yielding, good-quality, disease-resistant two-line hybrid water-saving and drought-resistance rice (WDR), hence promoting sustainable rice production in China.
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Affiliation(s)
- Yi Liu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Fenyun Zhang
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Xingxing Luo
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Deyan Kong
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Anning Zhang
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Feiming Wang
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Zhongquan Pan
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Jiahong Wang
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Junguo Bi
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China
| | - Guolan Liu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China.
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, People's Republic of China.
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Liu Z, Zhu Y, Shi H, Qiu J, Ding X, Kou Y. Recent Progress in Rice Broad-Spectrum Disease Resistance. Int J Mol Sci 2021; 22:11658. [PMID: 34769087 PMCID: PMC8584176 DOI: 10.3390/ijms222111658] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized.
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Affiliation(s)
- Zhiquan Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Yujun Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Huanbin Shi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China;
| | - Yanjun Kou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
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Genetic Improvement of Cereals and Grain Legumes. Genes (Basel) 2020; 11:genes11111255. [PMID: 33113769 PMCID: PMC7692374 DOI: 10.3390/genes11111255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to yield improvement is a better understanding of the genetic variation and identification of molecular markers, quantitative trait loci, genes, and pathways related to higher yields and increased tolerance to biotic and abiotic stresses. Advances in genetic technologies are enabling plant breeders and geneticists to breed crop plants with improved agronomic traits. This Special Issue is an effort to report the genetic improvements by adapting genomic techniques and genomic selection.
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