1
|
Gu Q, Lv X, Zhang D, Zhang Y, Wang X, Ke H, Yang J, Chen B, Wu L, Zhang G, Wang X, Sun Z, Ma Z. Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility. Genomics 2024; 116:110848. [PMID: 38663523 DOI: 10.1016/j.ygeno.2024.110848] [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] [Received: 01/27/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 06/03/2024]
Abstract
Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.
Collapse
Affiliation(s)
- Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Xing Lv
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Dongmei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Xingyi Wang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China.
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China.
| |
Collapse
|
2
|
Chen T, Miao Y, Jing F, Gao W, Zhang Y, Zhang L, Zhang P, Guo L, Yang D. Genomic-wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.). THE PLANT GENOME 2024:e20480. [PMID: 38840306 DOI: 10.1002/tpg2.20480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
Seven in absentia proteins, which contain a conserved SINA domain, are involved in regulating various aspects of wheat (Triticum aestivum L.) growth and development, especially in response to environmental stresses. However, it is unclear whether TaSINA family members are involved in regulating grain development until now. In this study, the expression pattern, genomic polymorphism, and relationship with grain-related traits were analyzed for all TaSINA members. Most of the TaSINA genes identified showed higher expression levels in young wheat spikes or grains than other organs. The genomic polymorphism analysis revealed that at least 62 TaSINA genes had different haplotypes, where the haplotypes of five genes were significantly correlated with grain-related traits. Kompetitive allele-specific PCR markers were developed to confirm the single nucleotide polymorphisms in TaSINA101 and TaSINA109 among the five selected genes in a set of 292 wheat accessions. The TaSINA101-Hap II and TaSINA109-Hap II haplotypes had higher grain weight and width compared to TaSINA101-Hap I and TaSINA109-Hap I in at least three environments, respectively. The qRT-PCR assays revealed that TaSINA101 was highly expressed in the palea shell, seed coat, and embryo in young wheat grains. The TaSINA101 protein was unevenly distributed in the nucleus when transiently expressed in the protoplast of wheat. Three homozygous TaSINA101 transgenic lines in rice (Oryza sativa L.) showed higher grain weight and size compared to the wild type. These findings provide valuable insight into the biological function and elite haplotype of TaSINA family genes in wheat grain development at a genomic-wide level.
Collapse
Affiliation(s)
- Tao Chen
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongping Miao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fanli Jing
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weidong Gao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yanyan Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Long Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Lijian Guo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
3
|
Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
Collapse
Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| |
Collapse
|
4
|
Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
Collapse
Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| |
Collapse
|
5
|
Yu H, Bhat JA, Li C, Zhao B, Bu M, Zhang Z, Guo T, Feng X. Identification of superior and rare haplotypes to optimize branch number in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:93. [PMID: 38570354 PMCID: PMC10991007 DOI: 10.1007/s00122-024-04596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE Using the integrated approach in the present study, we identified eleven significant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean. Branch number is a key yield-related quantitative trait that directly affects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs significantly associated with branch number across three environments using the five GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of ± 202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identified on nine different chromosomes. Haplotype allele number across the identified haplotype blocks varies from two to five, and different branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identified underlying the genomic region of ± 202.4 kb of the identified SNPs as putative candidates; and six of them showed significant differential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The findings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.
Collapse
Affiliation(s)
- Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Zhejiang Lab, Hangzhou, 310012, China
| | | | - Candong Li
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Beifang Zhao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Moran Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Tai Guo
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- Zhejiang Lab, Hangzhou, 310012, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
| |
Collapse
|
6
|
Tang W, Chen H, Zhang S, Tang J, Lin J, Fang X, Chen G, Zhang Y. A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:745. [PMID: 38475591 DOI: 10.3390/plants13050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.
Collapse
Affiliation(s)
- Weijie Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jun Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jing Lin
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
7
|
Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study. BMC PLANT BIOLOGY 2024; 24:124. [PMID: 38373874 PMCID: PMC10877931 DOI: 10.1186/s12870-024-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. RESULTS Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. CONCLUSIONS Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
Collapse
Grants
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
Collapse
Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India.
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | |
Collapse
|
8
|
Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [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] [Received: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
Collapse
Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. Multi-model genome-wide association studies for appearance quality in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1304388. [PMID: 38273959 PMCID: PMC10808671 DOI: 10.3389/fpls.2023.1304388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]
Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
Collapse
Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| |
Collapse
|
11
|
Liu G, Qiu D, Lu Y, Wu Y, Han X, Jiao Y, Wang T, Yang J, You A, Chen J, Zhang Z. Identification of Superior Haplotypes and Haplotype Combinations for Grain Size- and Weight-Related Genes for Breeding Applications in Rice ( Oryza sativa L.). Genes (Basel) 2023; 14:2201. [PMID: 38137023 PMCID: PMC10742856 DOI: 10.3390/genes14122201] [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: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The identification of superior haplotypes and haplotype combinations is essential for haplotype-based breeding (HBB), which provides selection targets for genomics-assisted breeding. In this study, genotypes of 42 functional genes in rice were analyzed by targeted capture sequencing in a panel of 180 Indica rice accessions. In total, 69 SNPs/Indels in seven genes were detected to be associated with grain length (GL), grain width (GW), ratio of grain length-width (L/W) and thousand-grain weight (TGW) using candidate gene-based association analysis, including BG1 and GS3 for GL, GW5 for GW, BG1 and GW5 for L/W, and AET1, SNAC1, qTGW3, DHD1 and GW5 for TGW. Furthermore, two haplotypes were identified for each of the seven genes according to these associated SNPs/Indels, and the amount of genetic variation explained by different haplotypes ranged from 3.24% to 27.66%. Additionally, three, three and eight haplotype combinations for GL, L/W and TGW explained 25.38%, 5.5% and 22.49% of the total genetic variation for each trait, respectively. Further analysis showed that Minghui63 had the superior haplotype combination Haplotype Combination 4 (HC4) for TGW. The most interesting finding was that some widely used restorer lines derived from Minghui63 also have the superior haplotype combination HC4, and our breeding varieties and lines using the haplotype-specific marker panel also confirmed that the TGW of the lines was much higher than that of their sister lines without HC4, suggesting that TGW-HC4 is the superior haplotype combination for TGW and can be utilized in rice breeding.
Collapse
Affiliation(s)
- Gang Liu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Dongfeng Qiu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Yuxia Lu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Yan Wu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuesong Han
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Yaru Jiao
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Tingbao Wang
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Jinsong Yang
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Aiqing You
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| | - Jianguo Chen
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zaijun Zhang
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (G.L.); (D.Q.); (Y.L.); (Y.W.); (X.H.); (Y.J.); (T.W.); (J.Y.); (A.Y.)
| |
Collapse
|
12
|
Joshi G, Soe YP, Palanog A, Hore TK, Nha CT, Calayugan MI, Inabangan-Asilo MA, Amparado A, Pandey ID, Cruz PCS, Hernandez JE, Swamy BPM. Meta-QTL s and haplotypes for efficient zinc biofortification of rice. THE PLANT GENOME 2023; 16:e20315. [PMID: 36896580 DOI: 10.1002/tpg2.20315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Biofortification of rice with improved grain zinc (Zn) content is the most sustainable and cost-effective approach to address Zn malnutrition in Asia. Genomics-assisted breeding using precise and consistent Zn quantitative trait loci (QTLs), genes, and haplotypes can fast-track the development of Zn biofortified rice varieties. We conducted the meta-analysis of 155 Zn QTLs reported from 26 different studies. Results revealed 57 meta-QTLs with a significant reduction of 63.2% and 80% in the number and confidence interval of the Zn QTLs, respectively. Meta-quantitative trait loci (MQTLs) regions were found to be enriched with diverse metal homeostasis genes; at least 11 MQTLs were colocated with 20 known major genes involved in the production of root exudates, metal uptake, transport, partitioning, and loading into grains in rice. These genes were differentially expressed in vegetative and reproductive tissues, and a complex web of interactions were observed among them. We identified superior haplotypes and their combinations for nine candidate genes (CGs), and the frequency and allelic effects of superior haplotypes varied in different subgroups. The precise MQTLs with high phenotypic variance, CGs, and superior haplotypes identified in our study are useful for an efficient Zn biofortification of rice and to ensure Zn as an essential component of all the future rice varieties through mainstreaming of Zn breeding.
Collapse
Affiliation(s)
- Gaurav Joshi
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | | | - Tapas Kumer Hore
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Chau Thanh Nha
- Philippines Rice Research Institute, Muñoz, Nueva Ecija, Philippines
| | | | - Mary Ann Inabangan-Asilo
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Amery Amparado
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Indra Deo Pandey
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | | | - B P Mallikarjuna Swamy
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| |
Collapse
|
13
|
Yamasani MR, Pandu VR, Kalluru S, Bommaka RR, Bandela R, Duddu B, Komeri S, Kumbha D, Vemireddy LR. Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions. Mol Biol Rep 2023; 50:8177-8188. [PMID: 37555871 DOI: 10.1007/s11033-023-08714-9] [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] [Received: 04/03/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. METHODS AND RESULTS In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. CONCLUSIONS In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
Collapse
Affiliation(s)
- Mounika Reddy Yamasani
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Vasanthi Raguru Pandu
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Rupeshkumar Reddy Bommaka
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Ramanamurthy Bandela
- Department of Statistics and Computer Applications, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Bharathi Duddu
- Department of Genetics and Plant Breeding, Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Srikanth Komeri
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Dineshkumar Kumbha
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India.
| |
Collapse
|
14
|
Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
Collapse
Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| |
Collapse
|
15
|
Sahoo B, Nayak I, Parameswaran C, Kesawat MS, Sahoo KK, Subudhi HN, Balasubramaniasai C, Prabhukarthikeyan SR, Katara JL, Dash SK, Chung SM, Siddiqui MH, Alamri S, Samantaray S. A Comprehensive Genome-Wide Investigation of the Cytochrome 71 ( OsCYP71) Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of OsCYP71P6 on Yield-Related Traits in Indica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3035. [PMID: 37687282 PMCID: PMC10490456 DOI: 10.3390/plants12173035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.
Collapse
Affiliation(s)
- Bijayalaxmi Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Ravenshaw University, Cuttack 753006, India;
| | - Itishree Nayak
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Utkal University, Bhubaneswar 751004, India
| | - C. Parameswaran
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri University, Cuttack 754006, India
| | | | - H. N. Subudhi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Cayalvizhi Balasubramaniasai
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | | | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sushanta Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sang-Min Chung
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea;
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Sanghamitra Samantaray
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| |
Collapse
|
16
|
Navea IP, Maung PP, Yang S, Han JH, Jing W, Shin NH, Zhang W, Chin JH. A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1226297. [PMID: 37662146 PMCID: PMC10471825 DOI: 10.3389/fpls.2023.1226297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice.
Collapse
Affiliation(s)
- Ian Paul Navea
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| | - Phyu Phyu Maung
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| | - Shiyi Yang
- College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jae-Hyuk Han
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- The International Rice Research Institute-Korea Office, National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Republic of Korea
| | - Wen Jing
- College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Na-Hyun Shin
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| | - Wenhua Zhang
- College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Joong Hyoun Chin
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| |
Collapse
|
17
|
Aung KM, Oo WH, Maung TZ, Min MH, Somsri A, Nam J, Kim KW, Nawade B, Lee CY, Chu SH, Park YJ. Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1225445. [PMID: 37560030 PMCID: PMC10407808 DOI: 10.3389/fpls.2023.1225445] [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: 05/19/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.
Collapse
Affiliation(s)
- Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Win Htet Oo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jungrye Nam
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Bhagwat Nawade
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan, Republic of Korea
| | - Sang-Ho Chu
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| |
Collapse
|
18
|
Wang Y, Liu H, Meng Y, Liu J, Ye G. Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1194119. [PMID: 37324692 PMCID: PMC10267709 DOI: 10.3389/fpls.2023.1194119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1 and Hap2, LOC_Os04g56950-Hap1, Hap2 and Hap8, LOC_Os07g24190-Hap3, LOC_Os12g12720-Hap3 and Hap6) and six superior haplotypes (LOC_Os02g17680-Hap2, Hap5 and Hap7, LOC_Os04g56950-Hap4, LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation.
Collapse
Affiliation(s)
- Yamei Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Agriculture, Sun Yat-sen University, Shenzhen, China
| | - Hongyan Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Yun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| |
Collapse
|
19
|
Xu T, Fu D, Xiong X, Zhu J, Feng Z, Liu X, Wu C. OsbHLH067, OsbHLH068, and OsbHLH069 redundantly regulate inflorescence axillary meristem formation in rice. PLoS Genet 2023; 19:e1010698. [PMID: 37053298 PMCID: PMC10128955 DOI: 10.1371/journal.pgen.1010698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 04/25/2023] [Accepted: 03/08/2023] [Indexed: 04/15/2023] Open
Abstract
Rice axillary meristems (AMs) are essential to the formation of tillers and panicle branches in rice, and therefore play a determining role in rice yield. However, the regulation of inflorescence AM development in rice remains elusive. In this study, we identified no spikelet 1-Dominant (nsp1-D), a sparse spikelet mutant, with obvious reduction of panicle branches and spikelets. Inflorescence AM deficiency in nsp1-D could be ascribed to the overexpression of OsbHLH069. OsbHLH069 functions redundantly with OsbHLH067 and OsbHLH068 in panicle AM formation. The Osbhlh067 Osbhlh068 Osbhlh069 triple mutant had smaller panicles and fewer branches and spikelets. OsbHLH067, OsbHLH068, and OsbHLH069 were preferentially expressed in the developing inflorescence AMs and their proteins could physically interact with LAX1. Both nsp1-D and lax1 showed sparse panicles. Transcriptomic data indicated that OsbHLH067/068/069 may be involved in the metabolic pathway during panicle AM formation. Quantitative RT-PCR results demonstrated that the expression of genes involved in meristem development and starch/sucrose metabolism was down-regulated in the triple mutant. Collectively, our study demonstrates that OsbHLH067, OsbHLH068, and OsbHLH069 have redundant functions in regulating the formation of inflorescence AMs during panicle development in rice.
Collapse
Affiliation(s)
- Tingting Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaohu Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Junkai Zhu
- Jiangsu Kingearth Seed Co., Ltd., Yangzhou, China
| | - Zhiyun Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaobin Liu
- Jiangsu Kingearth Seed Co., Ltd., Yangzhou, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
20
|
Yu H, Bhat JA, Li C, Zhao B, Guo T, Feng X. Genome-wide survey identified superior and rare haplotypes for plant height in the north-eastern soybean germplasm of China. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:22. [PMID: 37309452 PMCID: PMC10248691 DOI: 10.1007/s11032-023-01363-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/18/2023] [Indexed: 06/14/2023]
Abstract
The proper and efficient utilization of natural genetic diversity can significantly impact crop improvements. Plant height is a quantitative trait governing the plant type as well as the yield and quality of soybean. Here, we used a combined approach including a genome-wide association study (GWAS) and haplotype and candidate gene analyses to explore the genetic basis of plant height in diverse natural soybean populations. For the GWAS analysis, we used the whole-genome resequencing data of 196 diverse soybean cultivars collected from different accumulated temperature zones of north-eastern China to detect the significant single-nucleotide polymorphisms (SNPs) associated with plant height across three environments (E1, E2, and E3). A total of 33 SNPs distributed on four chromosomes, viz., Chr.02, Chr.04, Chr.06, and Chr.19, were identified to be significantly associated with plant height across the three environments. Among them, 23 were consistently detected in two or more environments and the remaining 10 were identified in only one environment. Interestingly, all the significant SNPs detected on the respective chromosomes fell within the physical interval of linkage disequilibrium (LD) decay (± 38.9 kb). Hence, these genomic regions were considered to be four quantitative trait loci (QTLs), viz., qPH2, qPH4, qPH6, and qPH19, regulating plant height. Moreover, the genomic region flanking all significant SNPs on four chromosomes exhibited strong LD. These significant SNPs thus formed four haplotype blocks, viz., Hap-2, Hap-4, Hap-6, and Hap-19. The number of haplotype alleles underlying each block varied from four to six, and these alleles regulate the different phenotypes of plant height ranging from dwarf to extra-tall heights. Nine candidate genes were identified within the four haplotype blocks, and these genes were considered putative candidates regulating soybean plant height. Hence, these stable QTLs, superior haplotypes, and candidate genes (after proper validation) can be deployed for the development of soybean cultivars with desirable plant heights. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01363-7.
Collapse
Affiliation(s)
- Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- Zhejiang Lab, Hangzhou, 310012 China
| | | | - Candong Li
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007 China
| | - Beifang Zhao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
| | - Tai Guo
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007 China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- Zhejiang Lab, Hangzhou, 310012 China
| |
Collapse
|
21
|
Zheng Y, Fu D, Yang Z. OsDPE2 Regulates Rice Panicle Morphogenesis by Modulating the Content of Starch. RICE (NEW YORK, N.Y.) 2023; 16:5. [PMID: 36732485 PMCID: PMC9895648 DOI: 10.1186/s12284-023-00618-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Starch is a carbon sink for most plants, and its biological role changes with response to the environment and during plant development. Disproportionating Enzyme 2 (DPE2) is a 4-α-glycosyltransferase involved in starch degradation in plants at night. LAX1 plays a vital role in axillary meristem initiation in rice. Herein, results showed that Oryza sativa Disproportionating Enzyme 2 (OsDPE2) could rescue the mutant phenotype of lax1-6, LAX1 mutant. OsDPE2 encodes rice DPE2 located in the cytoplasm. In this study, OsDPE2 affected the vegetative plant development of rice via DPE2 enzyme. Additionally, OsDPE2 regulated the reproductive plant development of rice by modulating starch content in young panicles. Furthermore, haplotype OsDPE2(AQ) with higher DPE2 enzyme activity increased the panicle yield of rice. In summary, OsDPE2 can regulate vegetative and reproductive plant development of rice by modulating starch content. Furthermore, DPE2 activities of OsDPE2 haplotypes are associated with the panicle yield of rice. This study provides guidance for rice breeding to improve panicle yield traits.
Collapse
Affiliation(s)
- Yi Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zenan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| |
Collapse
|
22
|
Rai M, Tyagi W. Haplotype breeding for unlocking and utilizing plant genomics data. Front Genet 2022; 13:1006288. [DOI: 10.3389/fgene.2022.1006288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
|
23
|
Ren R, Liu W, Yao M, Jia Y, Huang L, Li W, He X, Guan M, Liu Z, Guan C, Hua W, Xiong X, Qian L. Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:69. [PMID: 37313473 PMCID: PMC10248621 DOI: 10.1007/s11032-022-01337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/07/2022] [Indexed: 06/15/2023]
Abstract
Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01337-1.
Collapse
Affiliation(s)
- Rui Ren
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Min Yao
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Yuan Jia
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Luyao Huang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wenqian Li
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Zhongsong Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xinghua Xiong
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| |
Collapse
|
24
|
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]
|
25
|
Bhat JA, Karikari B, Adeboye KA, Ganie SA, Barmukh R, Hu D, Varshney RK, Yu D. Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2407-2422. [PMID: 35639109 PMCID: PMC9271120 DOI: 10.1007/s00122-022-04120-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Plant height of soybean is associated with a haplotype block on chromosome 19, which classified 211 soybean accessions into five distinct groups showing significant differences for the target trait. Genetic variation is pivotal for crop improvement. Natural populations are precious genetic resources. However, efficient strategies for the targeted utilization of these resources for quantitative traits, such as plant height (PH), are scarce. Being an important agronomic trait associated with soybean yield and quality, it is imperative to unravel the genetic mechanisms underlying PH in soybean. Here, a genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with PH in a natural population of 211 cultivated soybeans, which was genotyped with NJAU 355 K Soy SNP Array and evaluated across six environments. A total of 128 SNPs distributed across 17 chromosomes were found to be significantly associated with PH across six environments and a combined environment. Three significant SNPs were consistently identified in at least three environments on Chr.02 (AX-93958260), Chr.17 (AX-94154834), and Chr.19 (AX-93897200). Genomic regions of ~ 130 kb flanking these three consistent SNPs were considered as stable QTLs, which included 169 genes. Of these, 22 genes (including Dt1) were prioritized and defined as putative candidates controlling PH. The genomic region flanking 12 most significant SNPs was in strong linkage disequilibrium (LD). These SNPs formed a single haplotype block containing five haplotypes for PH, namely Hap-A, Hap-B, Hap-C, Hap-D, and Hap-E. Deployment of such superior haplotypes in breeding programs will enable development of improved soybean varieties with desirable plant height.
Collapse
Affiliation(s)
- Javaid Akhter Bhat
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China.
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Kehinde Adewole Adeboye
- Department of Agricultural Technology, Ekiti State Polytechnic, P. M. B. 1101, Isan, Nigeria
| | - Showkat Ahmad Ganie
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, USA
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Dezhou Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- Murdoch's Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
| | - Deyue Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
26
|
Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement. Int J Mol Sci 2022; 23:ijms23136929. [PMID: 35805930 PMCID: PMC9266455 DOI: 10.3390/ijms23136929] [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: 06/03/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Reproductive-stage heat stress (RSHS) poses a major constraint to cereal crop production by damaging main plant reproductive structures and hampering reproductive processes, including pollen and stigma viability, pollination, fertilization, grain setting and grain filling. Despite this well-recognized fact, research on crop heat stress (HS) is relatively recent compared to other abiotic stresses, such as drought and salinity, and in particular, RSHS studies in cereals are considerably few in comparison with seedling-stage and vegetative-stage-centered studies. Meanwhile, climate change-exacerbated HS, independently or synergistically with drought, will have huge implications on crop performance and future global food security. Fortunately, due to their sedentary nature, crop plants have evolved complex and diverse transient and long-term mechanisms to perceive, transduce, respond and adapt to HS at the molecular, cell, physiological and whole plant levels. Therefore, uncovering the molecular and physiological mechanisms governing plant response and tolerance to RSHS facilitates the designing of effective strategies to improve HS tolerance in cereal crops. In this review, we update our understanding of several aspects of RSHS in cereals, particularly impacts on physiological processes and yield; HS signal perception and transduction; and transcriptional regulation by heat shock factors and heat stress-responsive genes. We also discuss the epigenetic, post-translational modification and HS memory mechanisms modulating plant HS tolerance. Moreover, we offer a critical set of strategies (encompassing genomics and plant breeding, transgenesis, omics and agronomy) that could accelerate the development of RSHS-resilient cereal crop cultivars. We underline that a judicious combination of all of these strategies offers the best foot forward in RSHS tolerance improvement in cereals. Further, we highlight critical shortcomings to RSHS tolerance investigations in cereals and propositions for their circumvention, as well as some knowledge gaps, which should guide future research priorities. Overall, our review furthers our understanding of HS tolerance in plants and supports the rational designing of RSHS-tolerant cereal crop cultivars for the warming climate.
Collapse
|
27
|
Higgins J, Santos B, Khanh TD, Trung KH, Duong TD, Doai NTP, Hall A, Dyer S, Ham LH, Caccamo M, De Vega J. Genomic regions and candidate genes selected during the breeding of rice in Vietnam. Evol Appl 2022; 15:1141-1161. [PMID: 35899250 PMCID: PMC9309459 DOI: 10.1111/eva.13433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/28/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (FST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.
Collapse
Affiliation(s)
| | | | - Tran Dang Khanh
- Agriculture Genetics Institute (AGI) Hanoi Vietnam
- Vietnam National University of Agriculture Hanoi Vietnam
| | | | | | | | - Anthony Hall
- Earlham Institute Norwich Research Park Norwich UK
| | | | - Le Huy Ham
- Agriculture Genetics Institute (AGI) Hanoi Vietnam
| | | | - Jose De Vega
- Earlham Institute Norwich Research Park Norwich UK
| |
Collapse
|
28
|
Zhang Y, Wang Y, Sun X, Yuan J, Zhao Z, Gao J, Wen X, Tang F, Kang M, Abliz B, Zhang Z, Zhang H, Wang F, Li Z. Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice. PLANTS 2022; 11:plants11111498. [PMID: 35684271 PMCID: PMC9182821 DOI: 10.3390/plants11111498] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
Malate dehydrogenase (MDH) is widely present in nature and regulates plant growth and development, as well as playing essential roles, especially in abiotic stress responses. Nevertheless, there is no comprehensive knowledge to date on MDH family members in rice. In this study, a total of 12 MDH members in rice were identified through genome-wide analysis and divided into three groups on the basis of their phylogenetic relationship and protein-conserved motifs. Evolutionary analysis showed that MDH proteins from rice, maize and wheat shared a close phylogenetic relationship, and the MDH family was conserved in the long-term process of domestication. We identified two segmental duplication events involving four genes, which could be the major force driving the expansion of the OsMDH family. The expression profile, cis-regulatory elements and qRT-PCR results of these genes revealed that a few OsMDH showed high tissue specificity, almost all of which had stress response elements in the promoter region, and ten MDH members were significantly induced by salt stress. Through gene-based association analysis, we found a significant correlation between salt tolerance at the seedling stage and the genetic variation of OsMDH8.1 and OsMDH12.1. Additionally, we found that the polymorphism in the promoter region of OsMDH8.1 might be related to the salt tolerance of rice. This study aimed to provide valuable information on the functional study of the rice MDH gene family related to salt stress response and revealed that OsMDH8.1 might be an important gene for the cultivar improvement of salt tolerance in rice.
Collapse
Affiliation(s)
- Yanhong Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Yulong Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xingming Sun
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Yuan
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Zhiqiang Zhao
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Jie Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaorong Wen
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Fusen Tang
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Mintai Kang
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Buhaliqem Abliz
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fengbin Wang
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Correspondence: (F.W.); (Z.L.)
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Correspondence: (F.W.); (Z.L.)
| |
Collapse
|
29
|
Darwell CT, Wanchana S, Ruanjaichon V, Siangliw M, Thunnom B, Aesomnuk W, Toojinda T. riceExplorer: Uncovering the Hidden Potential of a National Genomic Resource Against a Global Database. FRONTIERS IN PLANT SCIENCE 2022; 13:781153. [PMID: 35574109 PMCID: PMC9100803 DOI: 10.3389/fpls.2022.781153] [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: 09/22/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Agricultural crop breeding programs, particularly at the national level, typically consist of a core panel of elite breeding cultivars alongside a number of local landrace varieties (or other endemic cultivars) that provide additional sources of phenotypic and genomic variation or contribute as experimental materials (e.g., in GWAS studies). Three issues commonly arise. First, focusing primarily on core development accessions may mean that the potential contributions of landraces or other secondary accessions may be overlooked. Second, elite cultivars may accumulate deleterious alleles away from nontarget loci due to the strong effects of artificial selection. Finally, a tendency to focus solely on SNP-based methods may cause incomplete or erroneous identification of functional variants. In practice, integration of local breeding programs with findings from global database projects may be challenging. First, local GWAS experiments may only indicate useful functional variants according to the diversity of the experimental panel, while other potentially useful loci-identifiable at a global level-may remain undiscovered. Second, large-scale experiments such as GWAS may prove prohibitively costly or logistically challenging for some agencies. Here, we present a fully automated bioinformatics pipeline (riceExplorer) that can easily integrate local breeding program sequence data with international database resources, without relying on any phenotypic experimental procedure. It identifies associated functional haplotypes that may prove more robust in determining the genotypic determinants of desirable crop phenotypes. In brief, riceExplorer evaluates a global crop database (IRRI 3000 Rice Genomes) to identify haplotypes that are associated with extreme phenotypic variation at the global level and recorded in the database. It then examines which potentially useful variants are present in the local crop panel, before distinguishing between those that are already incorporated into the elite breeding accessions and those only found among secondary varieties (e.g., landraces). Results highlight the effectiveness of our pipeline, identifying potentially useful functional haplotypes across the genome that are absent from elite cultivars and found among landraces and other secondary varieties in our breeding program. riceExplorer can automatically conduct a full genome analysis and produces annotated graphical output of chromosomal maps, potential global diversity sources, and summary tables.
Collapse
|
30
|
Vinarao R, Proud C, Snell P, Fukai S, Mitchell J. Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice ( Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109. FRONTIERS IN PLANT SCIENCE 2022; 13:873677. [PMID: 35574104 PMCID: PMC9100824 DOI: 10.3389/fpls.2022.873677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.
Collapse
Affiliation(s)
- Ricky Vinarao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher Proud
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, Australia
| | - Shu Fukai
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jaquie Mitchell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
31
|
Rana N, Kumawat S, Kumar V, Bansal R, Mandlik R, Dhiman P, Patil GB, Deshmukh R, Sharma TR, Sonah H. Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice. Cells 2022; 11:cells11071144. [PMID: 35406707 PMCID: PMC8998046 DOI: 10.3390/cells11071144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.
Collapse
Affiliation(s)
- Nitika Rana
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Surbhi Kumawat
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Virender Kumar
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Ruchi Bansal
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Rushil Mandlik
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Pallavi Dhiman
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Gunvant B. Patil
- Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA;
| | - Rupesh Deshmukh
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Tilak Raj Sharma
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Crop Science, Indian Council of Agriculture Research (ICAR), Krishi Bhavan, New Delhi 110001, India
| | - Humira Sonah
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Correspondence: ; Tel.: +91-6239715281
| |
Collapse
|
32
|
Hu G, Wu Y, Guo C, Lu D, Dong N, Chen B, Qiao Y, Zhang Y, Pan Q. Haplotype Analysis of Chloroplast Genomes for Jujube Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:841767. [PMID: 35360311 PMCID: PMC8961131 DOI: 10.3389/fpls.2022.841767] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/11/2022] [Indexed: 05/31/2023]
Abstract
Jujube (family Rhamnaceae) is an important economic fruit tree in China. In this study, we reported 26 chloroplast (cp) sequences of jujube using Illumina paired-end sequencing. The sequence length of cp genome was 161, 367-161, 849 bp, which was composed of a large single-copy region (89053-89437 bp) and a small single-copy region (19356-19362 bp) separated by a pair of reverse repeat regions (26478-26533 bp). Each cp genome encodes the same 130 genes, including 112 unique genes, being quite conserved in genome structure and gene sequence. A total of 118 single base substitutions (SNPs) and 130 InDels were detected in 65 jujube accessions. Phylogenetic and haplotype network construction methods were used to analyze the origin and evolution of jujube and its sour-tasting relatives. We detected 32 effective haplotypes, consisting of 20 unique jujube haplotypes and 9 unique sour-jujube haplotypes. Compared with sour-jujube, jujube showed greater haplotype diversity at the chloroplast DNA level. To cultivate crisp and sweet fruit varieties featuring strong resistance, by combining the characteristics of sour-jujube and cultivated jujube, three hybrid combinations were suggested for reciprocal crosses: "Dongzao" × "Jingzao39," "Dongzao" × "Jingzao60," "Dongzao" × "Jingzao28." This study provides the basis for jujube species' identification and breeding, and lays the foundation for future research.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yuping Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qinghua Pan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| |
Collapse
|
33
|
DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview. Foods 2022; 11:foods11030258. [PMID: 35159410 PMCID: PMC8834242 DOI: 10.3390/foods11030258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 02/07/2023] Open
Abstract
Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.
Collapse
|
34
|
Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
Collapse
Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
| |
Collapse
|
35
|
Talukdar P, Travis AJ, Hossain M, Islam MR, Norton GJ, Price AH. Identification of genomic loci regulating grain iron content in
aus
rice under two irrigation management systems. Food Energy Secur 2021; 11:e329. [PMID: 35866052 PMCID: PMC9286631 DOI: 10.1002/fes3.329] [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: 05/12/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/15/2022] Open
Abstract
Iron (Fe) deficiency is one of the common causes of anaemia in humans. Improving grain Fe in rice, therefore, could have a positive impact for humans worldwide, especially for those people who consume rice as a staple food. In this study, 225–269 accessions of the Bengal and Assam Aus Panel (BAAP) were investigated for their accumulation of grain Fe in two consecutive years in a field experiment under alternative wetting and drying (AWD) and continuous flooded (CF) irrigation. AWD reduced straw Fe by 40% and grain Fe by 5.5–13%. Genotype differences accounted for 35% of the variation in grain Fe, while genotype by irrigation interaction accounted for 12% of the variation in straw and grain Fe in year 1, with no significant interactions detected in year 2. Twelve rice accessions were identified as having high grain Fe for both years regardless of irrigation treatment, half of which were from BAAP aus subgroup 3 which prominently comes from Bangladesh. On average, subgroup 3 had higher grain Fe than the other four subgroups of aus. Genome‐wide association mapping identified 6 genomic loci controlling natural variation of grain Fe concentration in plants grown under AWD. For one QTL, nicotianamine synthase OsNAS3 is proposed as candidate for controlling natural variation of grain Fe in rice. The BAAP contains three haplotypes of OsNAS3 where one haplotype (detected in 31% of the individuals) increased grain Fe up to 11%. Haplotype analysis of this gene in rice suggests that the ability to detect the QTL is enhanced in the BAAP because the high Fe allele is balanced in aus, unlike indica and japonica subgroups.
Collapse
Affiliation(s)
- Partha Talukdar
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | | | - Mahmud Hossain
- Department of Soil Science Bangladesh Agricultural University Mymensingh Bangladesh
| | - Md Rafiqul Islam
- Department of Soil Science Bangladesh Agricultural University Mymensingh Bangladesh
| | - Gareth J. Norton
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Adam H. Price
- School of Biological Sciences University of Aberdeen Aberdeen UK
| |
Collapse
|
36
|
Varshney RK, Barmukh R, Roorkiwal M, Qi Y, Kholova J, Tuberosa R, Reynolds MP, Tardieu F, Siddique KHM. Breeding custom-designed crops for improved drought adaptation. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e202100017. [PMID: 36620433 PMCID: PMC9744523 DOI: 10.1002/ggn2.202100017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 01/11/2023]
Abstract
The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.
Collapse
Affiliation(s)
- Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia,State Agricultural Biotechnology Centre, Centre for Crop and Food InnovationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA,Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Roberto Tuberosa
- Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | | | - Francois Tardieu
- Université de Montpellier, INRAE, Laboratoire d'Ecophysiologie des Plantes sous Stress, EnvironnementauxMontpellierFrance
| | - Kadambot H. M. Siddique
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| |
Collapse
|
37
|
Varshney RK, Bohra A, Roorkiwal M, Barmukh R, Cowling WA, Chitikineni A, Lam HM, Hickey LT, Croser JS, Bayer PE, Edwards D, Crossa J, Weckwerth W, Millar H, Kumar A, Bevan MW, Siddique KHM. Fast-forward breeding for a food-secure world. Trends Genet 2021; 37:1124-1136. [PMID: 34531040 DOI: 10.1016/j.tig.2021.08.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms, leveraged by evolving machine learning tools, will help provide mechanistic explanations for complex plant traits. Targeted and rapid assembly of beneficial alleles using optimized breeding strategies and precise genome editing techniques could deliver ideal crops for the future. Realizing desired productivity gains in the field is imperative for securing an adequate future food supply for 10 billion people.
Collapse
Affiliation(s)
- Rajeev K Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch WA 6150, Western Australia, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Rutwik Barmukh
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, QLD, Australia
| | - Janine S Croser
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Philipp E Bayer
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harvey Millar
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Arvind Kumar
- Deputy Director General's Office, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
38
|
Liu J, Zhan J, Chen J, Lu X, Zhi S, Ye G. Validation of Genes Affecting Rice Grain Zinc Content Through Candidate Gene-Based Association Analysis. Front Genet 2021; 12:701658. [PMID: 34434221 PMCID: PMC8381382 DOI: 10.3389/fgene.2021.701658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/02/2021] [Indexed: 11/27/2022] Open
Abstract
Several key genes governing Zn homeostasis and grain zinc content (GZC) have been functionally characterized. However, the effects of these genes in diverse breeding populations have not been evaluated; thus, their availability in breeding is unclear. In this study, the effects of 65 genes related to rice zinc responses on GZC were evaluated using two panels of breeding lines, and the superior haplotypes were identified. One panel consisted of mega varieties from the International Rice Research Institute (IRRI), South Asia, and Southeast Asia (SEA), and the other panel is breeding lines/varieties from South China (SC). In addition, a multiparent advanced generation intercross (MAGIC) population, named as DC1, was also employed. Three analytical methods, single-locus mixed linear model (SL-MLM), multilocus random-SNP-effect mixed linear model (mrMLM), and haplotype-based association analysis (Hap-AA), were applied. OsIDEF1 (which explained 12.3% of the phenotypic variance) and OsZIFL7 (8.3-9.1%), OsZIP7 (18.9%), and OsIRT1 (17.9%) were identified by SL-MLM in SEA and SC, respectively, whereas no gene was significantly associated with GZC in DC1. In total, five (OsNRAMP6, OsYSL15, OsIRT1, OsIDEF1, and OsZIFL7, 7.70-15.39%), three (OsFRDL1, OsIRT1, and OsZIP7, 11.87-17.99%), and two (OsYSL7 and OsZIP7, 9.85-10.57%) genes were detected to be significantly associated with GZC in SEA, SC, and DC1 by mrMLM, respectively. Hap-AA indicated that Hap1-OsNRAMP5, Hap5-OsZIP4, Hap1-OsIRT1, Hap3-OsNRAMP6, Hap6-OsMTP1, and Hap6-OsYSL15 had the largest effects for GZC in SEA, whereas Hap3-OsOPT7, Hap4-OsIRT2, Hap4-OsZIP7, Hap5-OsIRT1, and Hap5-OsSAMS1 were the most significant in the SC population. Besides, superior alleles were also identified for the significant genes. The genes significantly associated with GZC and their superior haplotypes identified in different panels could be used in enhancing GZC through molecular breeding, which could further address the problem of Zn malnutrition among rice consumers.
Collapse
Affiliation(s)
- Jindong Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhui Zhan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jingguang Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Agriculture, Sun Yat-sen University, Guangzhou, China
| | - Xiang Lu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuai Zhi
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Strategic Innovation Platform, International Rice Research Institute, Makati, Philippines
| |
Collapse
|
39
|
Vasumathy SK, Alagu M. SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces. Mol Biol Rep 2021; 48:5943-5953. [PMID: 34319545 DOI: 10.1007/s11033-021-06595-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND As rice is the staple food for more than half of the world's population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement. METHODS AND RESULTS The present study revealed a high level of genetic diversity among the unexploited rice landraces cultivated by the farmers of Kerala. Twelve polymorphic markers detected a total of seventy- seven alleles with an average of 6.416 alleles per locus. Polymorphic Information Content (PIC) value ranged from 0.459 to 0.809, and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with a high value of 0.809. The current study indicated that the rice landraces are highly diverse with higher values of the adequate number of alleles, PIC, and Shannon information index. Utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome inherited together, and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study. CONCLUSIONS The present investigation revealed the genetic diversity of rice landraces and the haplotype analysis will open the way for genome-wide association studies, QTL identification, and marker-assisted selection in the unexplored rice landraces collected from Kerala.
Collapse
Affiliation(s)
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala, 671316, India.
| |
Collapse
|
40
|
Varshney RK, Bohra A, Yu J, Graner A, Zhang Q, Sorrells ME. Designing Future Crops: Genomics-Assisted Breeding Comes of Age. TRENDS IN PLANT SCIENCE 2021; 26:631-649. [PMID: 33893045 DOI: 10.1016/j.tplants.2021.03.010] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 05/18/2023]
Abstract
Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.
Collapse
Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crops Plant Research (IPK), Gatersleben, Germany
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| |
Collapse
|
41
|
Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A. Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 2021; 11:10082. [PMID: 33980871 PMCID: PMC8115083 DOI: 10.1038/s41598-021-87964-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/19/2021] [Indexed: 02/03/2023] Open
Abstract
Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.
Collapse
Affiliation(s)
- Ramchander Selvaraj
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Arun Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Vikas Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Sonali Vijay Habde
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Uma Maheshwar Singh
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Arvind Kumar
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India.
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India.
| |
Collapse
|
42
|
Zhang F, Wang C, Li M, Cui Y, Shi Y, Wu Z, Hu Z, Wang W, Xu J, Li Z. The landscape of gene-CDS-haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement. MOLECULAR PLANT 2021; 14:787-804. [PMID: 33578043 DOI: 10.1016/j.molp.2021.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/14/2021] [Accepted: 02/04/2021] [Indexed: 05/27/2023]
Abstract
Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice. We characterized the gene-coding sequence-haplotype (gcHap) diversity of 45 963 rice genes in 3010 rice accessions. With an average of 226 ± 390 gcHaps per gene in rice populations, rice genes could be classified into three main categories: 12 865 conserved genes, 10 254 subspecific differentiating genes, and 22 844 remaining genes. We found that 39 218 rice genes carry >255 179 major gcHaps of potential functional importance. Most (87.5%) of the detected gcHaps were specific to subspecies or populations. The inferred proto-ancestors of local landrace populations reconstructed from conserved predominant (ancient) gcHaps correlated strongly with wild rice accessions from the same geographic regions, supporting a multiorigin (domestication) model of Oryza sativa. Past breeding efforts generally increased the gcHap diversity of modern varieties and caused significant frequency shifts in predominant gcHaps of 14 266 genes due to independent selection in the two subspecies. Low frequencies of "favorable" gcHaps at most known genes related to rice yield in modern varieties suggest huge potential for rice improvement by mining and pyramiding of favorable gcHaps. The gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex traits. The rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future.
Collapse
Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Agronomy, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Chunchao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yanru Cui
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Zhichao Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Agronomy, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Agronomy, Anhui Agricultural University, Hefei, Anhui, 230036, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China.
| |
Collapse
|
43
|
Yu H, Li Q, Li Y, Yang H, Lu Z, Wu J, Zhang Z, Shahid MQ, Liu X. Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice. RICE (NEW YORK, N.Y.) 2021; 14:16. [PMID: 33547986 PMCID: PMC7867503 DOI: 10.1186/s12284-021-00459-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/28/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Neo-tetraploid rice (NTR) is a useful new germplasm that developed from the descendants of the autotetraploid rice (ATR) hybrids. NTR showed improved fertility and yield potential, and produced high yield heterosis when crossed with indica ATR for commercial utilization. However, their classification, population structure and genomic feature remain elusive. RESULTS Here, high-depth genome resequencing data of 15 NTRs and 18 ATRs, together with 38 publicly available data of diploid rice accessions, were analyzed to conduct classification, population structure and haplotype analyses. Five subpopulations were detected and NTRs were clustered into one independent group that was adjacent to japonica subspecies, which maybe the reason for high heterosis when NTRs crossed with indica ATRs. Haplotype patterns of 717 key genes that associated with yield and other agronomic traits were revealed in these NTRs. Moreover, a novel specific SNP variation was detected in the first exon of HSP101, a known heat-inducible gene, which was conserved in all NTRs but absent in ATRs, 3KRG and RiceVarMap2 databases. The novel allele was named as HSP101-1, which was confirmed to be a heat response factor by qRT-PCR, and knockout of HSP101-1 significantly decreased the thermotolerance capacity of NTR. Interestingly, HSP101-1 was also specifically expressed in the anthers of NTR at pre-meiotic and meiosis stages under optimal environment without heat stress, and its loss-of-function mutant showed significant decrease in fertility of NTR. CONCLUSION The construction of first genomic variation repository and the revelation of population structure provide invaluable information for optimizing the designs of tetraploid rice breeding. The detection of specific genomic variations offered useful genomic markers and new directions to resolve high fertility mechanism of NTR.
Collapse
Affiliation(s)
- Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Qihang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Yudi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Huijing Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Zemin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642 China
| |
Collapse
|
44
|
Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
Collapse
Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| |
Collapse
|
45
|
Sinha P, Singh VK, Saxena RK, Khan AW, Abbai R, Chitikineni A, Desai A, Molla J, Upadhyaya HD, Kumar A, Varshney RK. Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2482-2490. [PMID: 32455481 PMCID: PMC7680530 DOI: 10.1111/pbi.13422] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 05/05/2023]
Abstract
Haplotype-based breeding, a recent promising breeding approach to develop tailor-made crop varieties, deals with identification of superior haplotypes and their deployment in breeding programmes. In this context, whole genome re-sequencing data of 292 genotypes from pigeonpea reference set were mined to identify the superior haplotypes for 10 drought-responsive candidate genes. A total of 83, 132 and 60 haplotypes were identified in breeding lines, landraces and wild species, respectively. Candidate gene-based association analysis of these 10 genes on a subset of 137 accessions of the pigeonpea reference set revealed 23 strong marker-trait associations (MTAs) in five genes influencing seven drought-responsive component traits. Haplo-pheno analysis for the strongly associated genes resulted in the identification of most promising haplotypes for three genes regulating five component drought traits. The haplotype C. cajan_23080-H2 for plant weight (PW), fresh weight (FW) and turgid weight (TW), the haplotype C. cajan_30211-H6 for PW, FW, TW and dry weight (DW), the haplotype C. cajan_26230-H11 for FW and DW and the haplotype C. cajan_26230-H5 for relative water content (RWC) were identified as superior haplotypes under drought stress condition. Furthermore, 17 accessions containing superior haplotypes for three drought-responsive genes were identified. The identified superior haplotypes and the accessions carrying these superior haplotypes will be very useful for deploying haplotype-based breeding to develop next-generation tailor-made better drought-responsive pigeonpea cultivars.
Collapse
Affiliation(s)
- Pallavi Sinha
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| | - Vikas K. Singh
- International Rice Research Institute (IRRI)South‐Asia HubICRISAT CampusPatancheruTelangana StateIndia
| | - Rachit K. Saxena
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| | - Aamir W. Khan
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI)South‐Asia HubICRISAT CampusPatancheruTelangana StateIndia
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| | - Aarthi Desai
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| | - Johiruddin Molla
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
- Ghatal Rabindra Satabarsiki MahaVidyalayaPaschim MedinipurWest BengalIndia
| | - Hari D. Upadhyaya
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| | - Arvind Kumar
- International Rice Research Institute (IRRI)South‐Asia HubICRISAT CampusPatancheruTelangana StateIndia
- IRRI South Asia Regional CenterVaranasiIndia
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelangana StateIndia
| |
Collapse
|
46
|
Abbai R, Singh VK, Snowdon RJ, Kumar A, Schnurbusch T. Seeking Crops with Balanced Parts for the Ideal Whole. TRENDS IN PLANT SCIENCE 2020; 25:1189-1193. [PMID: 32958388 DOI: 10.1016/j.tplants.2020.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/27/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Crop domestication and breeding considerably increased productivity over centuries but unconsciously lowered 'selfish plant behavior' or individual plant fitness. Paradoxically, enhancing individual plant fitness is mistakenly equated with crop improvement. Because agriculture relies on community performance, embracing an agroecological genetics and genomics viewpoint might maximize communal yield by matching crop genotypes to target environments.
Collapse
Affiliation(s)
- Ragavendran Abbai
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South Asia Hub, Hyderabad, India
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Arvind Kumar
- IRRI-South Asia Regional Centre (ISARC), Varanasi, India
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany; Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, Germany.
| |
Collapse
|
47
|
Bohra A, Chand Jha U, Godwin ID, Kumar Varshney R. Genomic interventions for sustainable agriculture. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2388-2405. [PMID: 32875704 PMCID: PMC7680532 DOI: 10.1111/pbi.13472] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/21/2020] [Accepted: 08/16/2020] [Indexed: 05/05/2023]
Abstract
Agricultural production faces a Herculean challenge to feed the increasing global population. Food production systems need to deliver more with finite land and water resources while exerting the least negative influence on the ecosystem. The unpredictability of climate change and consequent changes in pests/pathogens dynamics aggravate the enormity of the challenge. Crop improvement has made significant contributions towards food security, and breeding climate-smart cultivars are considered the most sustainable way to accelerate food production. However, a fundamental change is needed in the conventional breeding framework in order to respond adequately to the growing food demands. Progress in genomics has provided new concepts and tools that hold promise to make plant breeding procedures more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing delineate breeding targets that could contribute to securing future food supply. In this review, we highlight key breakthroughs in plant genome sequencing and explain how the presence of these genome resources in combination with gene editing techniques has revolutionized the procedures of trait discovery and manipulation. Adoption of new approaches such as speed breeding, genomic selection and haplotype-based breeding could overcome several limitations of conventional breeding. We advocate that strengthening varietal release and seed distribution systems will play a more determining role in delivering genetic gains at farmer's field. A holistic approach outlined here would be crucial to deliver steady stream of climate-smart crop cultivars for sustainable agriculture.
Collapse
Affiliation(s)
- Abhishek Bohra
- ICAR‐Indian Institute of Pulses Research (IIPR)KanpurIndia
| | - Uday Chand Jha
- ICAR‐Indian Institute of Pulses Research (IIPR)KanpurIndia
| | - Ian D. Godwin
- Centre for Crop ScienceQueensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Rajeev Kumar Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthAustralia
| |
Collapse
|
48
|
Sagare DB, Abbai R, Jain A, Jayadevappa PK, Dixit S, Singh AK, Challa V, Alam S, Singh UM, Yadav S, Sandhu N, Kabade PG, Singh VK, Kumar A. More and more of less and less: Is genomics-based breeding of dry direct-seeded rice (DDSR) varieties the need of hour? PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2173-2186. [PMID: 32725933 PMCID: PMC7589319 DOI: 10.1111/pbi.13454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/07/2020] [Accepted: 07/13/2020] [Indexed: 06/02/2023]
Abstract
Rice is a staple food for half of the world's population. Changing climatic conditions, water and labour scarcity are the major challenges that shall limit future rice production. Dry direct-seeded rice (DDSR) is emerging as an efficient, resources conserving, mechanized, climate smart and economically viable strategy to be adopted as an alternative to puddled transplanted rice (TPR) with the potential to address the problem of labour-water shortages and ensure sustainable rice cultivation. Despite these benefits, several constraints obstruct the adoption of DDSR. In principle, the plant type for DDSR should be different from one for TPR, which could be achieved by developing rice varieties that combine the traits of upland and lowland varieties. In this context, recent advances in precise phenotyping and NGS-based trait mapping led to identification of promising donors and QTLs/genes for DDSR favourable traits to be employed in genomic breeding. This review discusses the important traits influencing DDSR, research studies to clarify the need for breeding DDSR-specific varieties to achieve enhanced grain yield, climate resilience and nutrition demand. We anticipate that in the coming years, genomic breeding for developing DDSR-specific varieties would be a regular practice and might be further strengthened by combining superior haplotypes regulating important DDSR traits by haplotype-based breeding.
Collapse
Affiliation(s)
- Deepti B. Sagare
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Abhinav Jain
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | | | - Shilpi Dixit
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Arun Kumar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | | | - Shamshad Alam
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Shailesh Yadav
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
| | | | - Pramod G. Kabade
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Arvind Kumar
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
- International Rice Research Institute (IRRI)South‐Asia Regional Centre (SARC)VaranasiIndia
| |
Collapse
|
49
|
Kim KD, Kang Y, Kim C. Application of Genomic Big Data in Plant Breeding:Past, Present, and Future. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1454. [PMID: 33126607 PMCID: PMC7694055 DOI: 10.3390/plants9111454] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023]
Abstract
Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.
Collapse
Affiliation(s)
- Kyung Do Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea;
| | - Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea;
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea;
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea
| |
Collapse
|
50
|
Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
Collapse
Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
| |
Collapse
|