1
|
Guha PK, Magar ND, Kommana M, Barbadikar KM, Suneel B, Gokulan C, Lakshmi DV, Patel HK, Sonti RV, Sundaram RM, Madhav MS. Strong culm: a crucial trait for developing next-generation climate-resilient rice lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:665-686. [PMID: 38737321 PMCID: PMC11087419 DOI: 10.1007/s12298-024-01445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.
Collapse
Affiliation(s)
- Pritam Kanti Guha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Nakul D. Magar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Madhavilatha Kommana
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Kalyani M. Barbadikar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B. Suneel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. Gokulan
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - D. Vijay Lakshmi
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Hitendra Kumar Patel
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V. Sonti
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - R. M. Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Maganti Sheshu Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- ICAR-Central Tobacco Research Institute, Rajahmundry, India
| |
Collapse
|
2
|
Sowadan O, Xu S, Li Y, Muleke EM, Sitoe HM, Dang X, Jiang J, Dong H, Hong D. Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice ( Oryza sativa L.). Genes (Basel) 2024; 15:105. [PMID: 38254994 PMCID: PMC10815206 DOI: 10.3390/genes15010105] [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: 12/14/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.
Collapse
Affiliation(s)
- Ognigamal Sowadan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Shanbin Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Yulong Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Institute of Crop Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Everlyne Mmbone Muleke
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Department of Agriculture and Land Use Management, School of Agriculture, Veterinary Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega P.O. Box 190-50100, Kenya
| | - Hélder Manuel Sitoe
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Faculty of Agronomy and Biological Sciences, Púngue University, P.O. Box 323, Manica 2202, Mozambique
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (X.D.); (J.J.)
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (X.D.); (J.J.)
| | - Hui Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Delin Hong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| |
Collapse
|
3
|
Liang C, Li Y, Zhang K, Wu Z, Liu J, Liu J, Zhou C, Wang S, Li F, Sui G. Selection and Yield Formation Characteristics of Dry Direct Seeding Rice in Northeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3496. [PMID: 37836236 PMCID: PMC10575160 DOI: 10.3390/plants12193496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Dry direct seeding rice (DSR) is an emerging production system because of increasing labor and water scarcity in rice cultivation. The limited availability of rice cultivars suitable for dry direct seeding hampers the widespread adoption of this cultivation method in Northeast China. This study aimed to investigate grain production and plant characteristics associated with dry direct seeding rice. We conducted a field experiment on 79 japonica rice cultivars in Shenyang City, Liaoning Province, Northeast China, in 2020 and 2021. This study found that the grain yield of the tested rice cultivars ranged from 5.75-11.00 t ha-1, with a growth duration lasting between 144-161 days across the cultivars. These cultivars were then categorized into high yielding (HY), medium yielding (MY), and low yielding (LY) based on daily yield by using Ward's hierarchical clustering method. The higher grain yield for HY compared to MY and LY was attributed to more spikelets per unit area. The HY alleviated the conflict between higher panicle density and larger panicle size by improving the seedling emergence rate and productive stem rate. It also significantly increased shoot biomass at maturity. The HY reduced the period between seeding and beginning of heading (BBCH 51) and the proportion of dry matter partitioned to the leaf at the heading stage. However, it also increased the accumulation of dry matter in the grain and the proportion of dry matter partitioned to the grain at maturity. Furthermore, the HY markedly increased the harvest index and grain-leaf ratio, which are beneficial to coordinate the source-sink relationship. A quadratic function predicted that 98 days is the optimum growth duration before heading (BBCH 51) for achieving maximum yield. In conclusion, for dry direct seeding rice, it is appropriate to select high-yielding japonica inbred rice cultivars with shorter growth duration before heading (about 93-102 day), higher panicle number (about 450-500 × 104 ha-1), more spikelet number per panicle (about 110-130), higher seedling emergence rate (about 70-75%), higher productive stem rate (about 60-70%), and greater harvest index (about 50-55%).
Collapse
Affiliation(s)
- Chao Liang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Yimeng Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Kunhao Zhang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Zhouzhou Wu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Jiaxin Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Junfeng Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Chanchan Zhou
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Guomin Sui
- Liaoning Academy of Agricultural Sciences, Shenyang 110161, China;
| |
Collapse
|
4
|
Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [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: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
Collapse
Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
| |
Collapse
|
5
|
Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [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: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
Collapse
Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| |
Collapse
|
6
|
Zhao DD, Jang YH, Kim EG, Park JR, Jan R, Lubna, Asaf S, Asif S, Farooq M, Chung H, Kang DJ, Kim KM. Identification of a Major Locus for Lodging Resistance to Typhoons Using QTL Analysis in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:449. [PMID: 36771534 PMCID: PMC9919122 DOI: 10.3390/plants12030449] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 09/10/2023]
Abstract
We detected a new target quantitative trait locus (QTL) for lodging resistance in rice by analyzing lodging resistance to typhoons (Maysak and Haishen) using a scale from 0 (no prostrating) to 1 (little prostrating or prostrating) to record the resistance score in a Cheongcheong/Nagdong double haploid rice population. Five quantitative trait loci for lodging resistance to typhoons were detected. Among them, qTyM6 and qTyH6 exhibited crucial effects of locus RM3343-RM20318 on chromosome 6, which overlaps with our previous rice lodging studies for the loci qPSLSA6-2, qPSLSB6-5, and qLTI6-2. Within the target locus RM3343-RM20318, 12 related genes belonging to the cytochrome P450 protein family were screened through annotation. Os06g0599200 (OsTyM/Hq6) was selected for further analysis. We observed that the culm and panicle lengths were positively correlated with lodging resistance to typhoons. However, the yield was negatively correlated with lodging resistance to typhoons. The findings of this study improve an understanding of rice breeding, particularly the culm length, early maturing, and heavy panicle varieties, and the mechanisms by which the plant's architecture can resist natural disasters such as typhoons to ensure food safety. These results also provide the insight that lodging resistance in rice may be associated with major traits such as panicle length, culm length, tiller number, and heading date, and thereby improvements in these traits can increase lodging resistance to typhoons. Moreover, rice breeding should focus on maintaining suitable varieties that can withstand the adverse effects of climate change in the future and provide better food security.
Collapse
Affiliation(s)
- Dan-Dan Zhao
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Crop Foundation Research Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Yoon-Hee Jang
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eun-Gyeong Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Ryoung Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Lubna
- Natural and Medical Science Research Center, University of Nizwa, Nizwa 616, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, Nizwa 616, Oman
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Muhammad Farooq
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyunjung Chung
- Crop Foundation Research Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dong-Jin Kang
- Teaching and Research Center for Bio-Coexistence, Faculty of Agriculture and Life Science, Hirosaki University, Gosyogawara 037-0202, Japan
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
7
|
Taniguchi S, Sakamoto T, Imase R, Nonoue Y, Tsunematsu H, Goto A, Matsushita K, Ohmori S, Maeda H, Takeuchi Y, Ishii T, Yonemaru JI, Ogawa D. Prediction of heading date, culm length, and biomass from canopy-height-related parameters derived from time-series UAV observations of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:998803. [PMID: 36582650 PMCID: PMC9792801 DOI: 10.3389/fpls.2022.998803] [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: 07/20/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Unmanned aerial vehicles (UAVs) are powerful tools for monitoring crops for high-throughput phenotyping. Time-series aerial photography of fields can record the whole process of crop growth. Canopy height (CH), which is vertical plant growth, has been used as an indicator for the evaluation of lodging tolerance and the prediction of biomass and yield. However, there have been few attempts to use UAV-derived time-series CH data for field testing of crop lines. Here we provide a novel framework for trait prediction using CH data in rice. We generated UAV-based digital surface models of crops to extract CH data of 30 Japanese rice cultivars in 2019, 2020, and 2021. CH-related parameters were calculated in a non-linear time-series model as an S-shaped plant growth curve. The maximum saturation CH value was the most important predictor for culm length. The time point at the maximum CH contributed to the prediction of days to heading, and was able to predict stem and leaf weight and aboveground weight, possibly reflecting the association of biomass with duration of vegetative growth. These results indicate that the CH-related parameters acquired by UAV can be useful as predictors of traits typically measured by hand.
Collapse
Affiliation(s)
- Shoji Taniguchi
- Research Center for Agricultural Information Technology, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Toshihiro Sakamoto
- Institute for Agro-Environmental Sciences, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Ryoji Imase
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Akitoshi Goto
- Research Center for Agricultural Information Technology, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Kei Matsushita
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Sinnosuke Ohmori
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Hideo Maeda
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yoshinobu Takeuchi
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Takuro Ishii
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Jun-ichi Yonemaru
- Research Center for Agricultural Information Technology, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| |
Collapse
|
8
|
Bisht D, Kumar N, Singh Y, Malik R, Djalovic I, Dhaka NS, Pal N, Balyan P, Mir RR, Singh VK, Dhankher OP, Kumar U, Kumar S. Effect of stem structural characteristics and cell wall components related to stem lodging resistance in a newly identified mutant of hexaploid wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1067063. [PMID: 36483946 PMCID: PMC9723335 DOI: 10.3389/fpls.2022.1067063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
In wheat, lodging is affected by anatomical and chemical characteristics of the stem cell wall. Plant characteristics determining the stem strength were measured in lodging tolerant mutant (PMW-2016-1) developed through mutation breeding utilizing hexaploid wheat cultivar, DPW-621-50. Various anatomical features, chemical composition, and mechanical strength of the culms of newly developed lodging-tolerant mutant (PMW-2016-1) and parent (DPW-621-50), were examined by light microscopy, the Klason method, prostate tester coupled with a Universal Tensile Machine, and Fourier Transform Infrared Spectroscopy. Significant changes in the anatomical features, including the outer radius of the stem, stem wall thickness, and the proportions of various tissues, and vascular bundles were noticed. Chemical analysis revealed that the lignin level in the PMW-2016-1 mutant was higher and exhibited superiority in stem strength compared to the DPW-621-50 parent line. The force (N) required to break the internodes of mutant PMW-2016-1 was higher than that of DPW-621-50. The results suggested that the outer stem radius, stem wall thickness, the proportion of sclerenchyma tissues, the number of large vascular bundles, and lignin content are important factors that affect the mechanical strength of wheat stems, which can be the key parameters for the selection of varieties having higher lodging tolerance. Preliminary studies on the newly identified mutant PMW-2016-1 suggested that this mutant may possess higher lodging tolerance because it has a higher stem strength than DPW-621-50 and can be used as a donor parent for the development of lodging-tolerant wheat varieties.
Collapse
Affiliation(s)
- Darshana Bisht
- Molecular Cytogenetics Laboratory, Department of Molecular Biology & Genetic Engineering, College of Basic Science & Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Naveen Kumar
- Molecular Cytogenetics Laboratory, Department of Molecular Biology & Genetic Engineering, College of Basic Science & Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Yogita Singh
- Department of Molecular Biology & Biotechnology, College of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Rashmi Malik
- Department of Genetics & Plant Breeding, College of Agriculture, Govind Ballabh Pant University of Agriculture & Technology, Pantnagar, India
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - Narendra Singh Dhaka
- Department of Genetics & Plant Breeding, College of Agriculture, Govind Ballabh Pant University of Agriculture & Technology, Pantnagar, India
| | - Neeraj Pal
- Molecular Cytogenetics Laboratory, Department of Molecular Biology & Genetic Engineering, College of Basic Science & Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri Post Graduate College, CCS University, Meerut, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, India
| | - Vinay Kumar Singh
- Department of Mechanical Engineering, College of Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, United States
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology, College of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Sundip Kumar
- Molecular Cytogenetics Laboratory, Department of Molecular Biology & Genetic Engineering, College of Basic Science & Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| |
Collapse
|
9
|
Dreccer MF, Macdonald B, Farnsworth CA, Paccapelo MV, Awasi MA, Condon AG, Forrest K, Lee Long I, McIntyre CL. Multi-donor × elite-based populations reveal QTL for low-lodging wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1685-1703. [PMID: 35312799 PMCID: PMC9110543 DOI: 10.1007/s00122-022-04063-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/12/2022] [Indexed: 05/15/2023]
Abstract
Low-lodging high-yielding wheat germplasm and SNP-tagged novel alleles for lodging were identified in a process that involved selecting donors through functional phenotyping for underlying traits with a designed phenotypic screen, and a crossing strategy involving multiple-donor × elite populations. Lodging is a barrier to achieving high yield in wheat. As part of a study investigating the potential to breed low-lodging high-yielding wheat, populations were developed crossing four low-lodging high-yielding donors selected based on lodging related traits, with three cultivars. Lodging was evaluated in single rows in an early generation and subsequently in plots in 2 years with contrasting lodging environment. A large number of lines lodged less than their recurrent parents, and some were also higher yielding. Heritability for lodging was high, but the genetic correlation between contrasting environments was intermediate-low. Lodging genotypic rankings in single rows did not correlate well with plots. Populations from the highest lodging background were genotyped (90 K iSelect BeadChip array). Fourteen markers on nine chromosomes were associated with lodging, differing under high- versus low-lodging conditions. Of the fourteen markers, ten were found to co-locate with previously identified QTL for lodging-related traits or at homoeologous locations for previously identified lodging-related QTL, while the remaining four markers (in chromosomes 2D, 4D, 7B and 7D) appear to map to novel QTL for lodging. Lines with more favourable markers lodged less, suggesting value in these markers as a selection tool. This study demonstrates that the combination of donor functional phenotyping, screen design and crossing strategy can help identify novel alleles in germplasm without requiring extensive bi-parental populations.
Collapse
Affiliation(s)
- M Fernanda Dreccer
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia.
| | - Bethany Macdonald
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Claire A Farnsworth
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - M Valeria Paccapelo
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Mary Anne Awasi
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - Anthony G Condon
- CSIRO Agriculture and Food, Building 101, Clunies Ross Street, Black Mountain, ACT, 2600, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Ian Lee Long
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - C Lynne McIntyre
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| |
Collapse
|
10
|
Sandhu N, Singh J, Singh G, Sethi M, Singh MP, Pruthi G, Raigar OP, Kaur R, Kaur R, Sarao PS, Lore JS, Singh UM, Dixit S, Sagare DB, Singh S, Satturu V, Singh VK, Kumar A. Development and validation of a novel core set of KASP markers for the traits improving grain yield and adaptability of rice under direct-seeded cultivation conditions. Genomics 2022; 114:110269. [DOI: 10.1016/j.ygeno.2022.110269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/12/2021] [Accepted: 01/16/2022] [Indexed: 11/28/2022]
|
11
|
Heredia MC, Kant J, Prodhan MA, Dixit S, Wissuwa M. Breeding rice for a changing climate by improving adaptations to water saving technologies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:17-33. [PMID: 34218290 DOI: 10.1007/s00122-021-03899-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
Collapse
Affiliation(s)
| | | | - M Asaduzzaman Prodhan
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, The Philippines
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
| |
Collapse
|
12
|
Potupureddi G, Balija V, Ballichatla S, C. G. G, Awalellu K, Lekkala S, Jallipalli K, M. G. G, Mohammad E, M M, Arutla S, Burka R, Gouri Shankar L, Ayyangari Phani P, Lella Venkata S, Raman Meenakshi S, B. C. V, Vemuri RB, Brahma K, Madnala R, Patel HK, Sonti RV, Madhav MS. Mutation resource of Samba Mahsuri revealed the presence of high extent of variations among key traits for rice improvement. PLoS One 2021; 16:e0258816. [PMID: 34669755 PMCID: PMC8528289 DOI: 10.1371/journal.pone.0258816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
To create novel variants for morphological, physiological, and biotic stress tolerance traits, induced mutations were created using Ethyl Methane Sulphonate (EMS) in the background of Samba Mahsuri (BPT 5204), a popular and mega rice variety of India. A population derived from 10, 500 M1 plants and their descendants were phenotyped for a wide range of traits leading to the identification of 124 mutants having variations in key agro-morphological traits, and 106 mutants exhibiting variation for physiological traits. Higher yield is the ultimate goal of crop improvement and we identified 574 mutants having higher yield compared to wild type by having better yield attributing traits. Further, a total of 50 mutants showed better panicle exertion phenotypes as compared to Samba Mahsuri leading to enhancement of yield. Upon rigorous screening for three major biotic stresses, 8 mutants showed enhanced tolerance for yellow stem borer (YSB), and 13 different mutants each showed enhanced tolerance for sheath blight (ShB) and bacterial leaf blight (BLB), respectively. In addition, screening at multiple locations that have diverse field isolates identified 3, 3, and 5 lines for tolerance to ShB, YSB and BLB, respectively. On the whole, 1231 desired mutant lines identified at M2 were forwarded to an advanced generation (M5). PCR based allele mining indicated that the BLB tolerant mutants have a different allele than the reported alleles for well-known genes affecting bacterial blight resistance. Whole genome re-sequencing revealed substantial variation in comparison to Samba Mahsuri. The lines showing enhanced tolerance to important biotic stresses (YSB, ShB and BLB) as well as several economically important traits are unique genetic resources which can be utilized for the identification of novel genes/alleles for different traits. The lines which have better agronomic features can be used as pre-breeding lines. The entire mutant population is maintained as a national resource for genetic improvement of the rice crop.
Collapse
Affiliation(s)
- Gopi Potupureddi
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Vishalakshi Balija
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Suneel Ballichatla
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Gokulan C. G.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Komal Awalellu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Swathi Lekkala
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Karteek Jallipalli
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Gayathri M. G.
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Ershad Mohammad
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Milton M
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Srikanth Arutla
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Rajender Burka
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Laha Gouri Shankar
- Crop Protection, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | | | | | | | - Viraktamath B. C.
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | | | - Kranthi Brahma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Raju Madnala
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | | |
Collapse
|
13
|
Sandhu N, Yadav S, Catolos M, Cruz MTS, Kumar A. Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:637488. [PMID: 33936127 PMCID: PMC8082028 DOI: 10.3389/fpls.2021.637488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
There is an urgent need to breed dry direct-seeded adapted rice varieties in order to address the emerging scenario of water-labor shortage. The aim of this study was to develop high-yielding, direct-seeded adapted varieties utilizing biparental to multiparental crosses involving as many as six different parents in conventional breeding programs and 12 parents in genomics-assisted breeding programs. The rigorous single plant selections were followed from the F2 generation onwards utilizing phenotypic selection and quantitative trait locus (QTL)/gene-based/linked markers for tracking the presence of desirable alleles of targeted QTL/genes. In conventional breeding, multiparent lines had significantly higher yields (2,072-6,569 kg ha-1) than the biparental lines (1,493-6,326 kg ha-1). GAB lines derived from multiparent crosses had significantly higher (3,293-6,719 kg ha-1) yields than the multiparent lines from conventional breeding (2,072-6,569 kg ha-1). Eleven promising lines from genomics-assisted breeding carrying 7-11 QTL/genes and eight lines from conventional breeding with grain-yield improvement from 727 to 1,705 kg ha-1 and 68 to 902 kg ha-1, respectively, over the best check were selected. The developed lines may be released as varieties/parental lines to develop better rice varieties for direct-seeded situations or as novel breeding material to study genetic interactions.
Collapse
Affiliation(s)
- Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- International Rice Research Institute South Asia Regional Centre, Varanasi, India
| |
Collapse
|
14
|
Guo Z, Liu X, Zhang B, Yuan X, Xing Y, Liu H, Luo L, Chen G, Xiong L. Genetic analyses of lodging resistance and yield provide insights into post-Green-Revolution breeding in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:814-829. [PMID: 33159401 PMCID: PMC8051602 DOI: 10.1111/pbi.13509] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 10/22/2020] [Accepted: 11/01/2020] [Indexed: 05/10/2023]
Abstract
Lodging reduces grain yield in cereal crops. Understanding the genetic basis of lodging resistance (LR) benefits LR breeding. In the study, 524 accessions from a rice germplasm collection and 193 recombinant inbred lines were phenotyped for 17 LR-related traits. Height and culm strength (the magnitude of applied force necessary to break the culm) were two major factors affecting LR. We conducted genome-wide association study (GWAS) and identified 127 LR-associated loci. Significant phenotypic correlations between culm-strength traits and yield-related traits were observed. To reveal the genetic relationship between them, we conducted GWAS of culm-strength traits with adding yield-related trait as a covariate and detected 63 loci linking culm strength and yield. As a proof, a near-isogenic line for an association locus on chromosome 7 showed enhanced LR and yield. Strikingly, 58 additional loci were identified in the covariate-added GWAS. Several LR-associated loci had undergone divergent selection. Linkage analysis supported the GWAS results. We propose that introgression of alleles beneficial for both culm strength and panicle weight without negative effects on panicle number or pyramiding high-yielding alleles and lodging-resistant alleles without effects on yield can be employed for the post-Green-Revolution breeding.
Collapse
Affiliation(s)
- Zilong Guo
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
- Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiao Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanChina
| | - Bo Zhang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Xinjie Yuan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanChina
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Hongyan Liu
- Shanghai Agrobiological Gene CenterShanghaiChina
| | - Lijun Luo
- Shanghai Agrobiological Gene CenterShanghaiChina
| | - Guoxing Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanChina
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
15
|
Raza A, Asghar MA, Ahmad B, Bin C, Iftikhar Hussain M, Li W, Iqbal T, Yaseen M, Shafiq I, Yi Z, Ahmad I, Yang W, Weiguo L. Agro-Techniques for Lodging Stress Management in Maize-Soybean Intercropping System-A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1592. [PMID: 33212960 PMCID: PMC7698466 DOI: 10.3390/plants9111592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 11/24/2022]
Abstract
Lodging is one of the most chronic restraints of the maize-soybean intercropping system, which causes a serious threat to agriculture development and sustainability. In the maize-soybean intercropping system, shade is a major causative agent that is triggered by the higher stem length of a maize plant. Many morphological and anatomical characteristics are involved in the lodging phenomenon, along with the chemical configuration of the stem. Due to maize shading, soybean stem evolves the shade avoidance response and resulting in the stem elongation that leads to severe lodging stress. However, the major agro-techniques that are required to explore the lodging stress in the maize-soybean intercropping system for sustainable agriculture have not been precisely elucidated yet. Therefore, the present review is tempted to compare the conceptual insights with preceding published researches and proposed the important techniques which could be applied to overcome the devastating effects of lodging. We further explored that, lodging stress management is dependent on multiple approaches such as agronomical, chemical and genetics which could be helpful to reduce the lodging threats in the maize-soybean intercropping system. Nonetheless, many queries needed to explicate the complex phenomenon of lodging. Henceforth, the agronomists, physiologists, molecular actors and breeders require further exploration to fix this challenging problem.
Collapse
Affiliation(s)
- Ali Raza
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Ahsan Asghar
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhou 610000, China;
| | - Bushra Ahmad
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Punjab, Pakistan;
| | - Cheng Bin
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - M. Iftikhar Hussain
- Department of Plant Biology & Soil Science, Universidad de Vigo, 36310 Vigo, Spain;
| | - Wang Li
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Tauseef Iqbal
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Yaseen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China;
| | - Iram Shafiq
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhang Yi
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Irshan Ahmad
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenyu Yang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Liu Weiguo
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China; (A.R.); (C.B.); (W.L.); (T.I.); (I.S.); (Z.Y.); (I.A.); (W.Y.)
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
16
|
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
|
17
|
Li M, Hameed I, Cao D, He D, Yang P. Integrated Omics Analyses Identify Key Pathways Involved in Petiole Rigidity Formation in Sacred Lotus. Int J Mol Sci 2020; 21:ijms21145087. [PMID: 32708483 PMCID: PMC7404260 DOI: 10.3390/ijms21145087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022] Open
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a relic aquatic plant with two types of leaves, which have distinct rigidity of petioles. Here we assess the difference from anatomic structure to the expression of genes and proteins in two petioles types, and identify key pathways involved in petiole rigidity formation in sacred lotus. Anatomically, great variation between the petioles of floating and vertical leaves were observed. The number of collenchyma cells and thickness of xylem vessel cell wall was higher in the initial vertical leaves’ petiole (IVP) compared to the initial floating leaves’ petiole (IFP). Among quantified transcripts and proteins, 1021 and 401 transcripts presented 2-fold expression increment (named DEGs, genes differentially expressed between IFP and IVP) in IFP and IVP, 421 and 483 proteins exhibited 1.5-fold expression increment (named DEPs, proteins differentially expressed between IFP and IVP) in IFP and IVP, respectively. Gene function and pathway enrichment analysis displayed that DEGs and DEPs were significantly enriched in cell wall biosynthesis and lignin biosynthesis. In consistent with genes and proteins expressions in lignin biosynthesis, the contents of lignin monomers precursors were significantly different in IFP and IVP. These results enable us to understand lotus petioles rigidity formation better and provide valuable candidate genes information on further investigation.
Collapse
Affiliation(s)
- Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (M.L.); (D.H.)
| | - Ishfaq Hameed
- Departments of Botany, University of Chitral, Chitral 17200, Khyber Pukhtunkhwa, Pakistan;
| | - Dingding Cao
- Institue of Oceanography, Minjiang University, Fuzhou 350108, China;
| | - Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (M.L.); (D.H.)
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (M.L.); (D.H.)
- Correspondence:
| |
Collapse
|
18
|
Long W, Dan D, Yuan Z, Chen Y, Jin J, Yang W, Zhang Z, Li N, Li S. Deciphering the Genetic Basis of Lodging Resistance in Wild Rice Oryza longistaminata. FRONTIERS IN PLANT SCIENCE 2020; 11:628. [PMID: 32547576 PMCID: PMC7274161 DOI: 10.3389/fpls.2020.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/23/2020] [Indexed: 05/27/2023]
Abstract
The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the quantitative trait loci (QTLs)/genes for lodging resistance breeding. Oryza longistaminata exhibits a strong stem and high biomass productivity, which could be a candidate gene pool for cultivars lodging resistance improvement. Here, a set of 152 BC2F20 lines derived from a cross between a cultivated line 93-11 and O. longistaminata was evaluated for lodging resistance. QTL mapping analysis combined with single-nucleotide polymorphism (SNP) marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL), and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were first identified from O. longistaminata. A major QTL, qLR1, which was delimited to a region ∼80 kb on chromosome 1, increased stem diameter, stem length, and breaking strength. Another major QTL, qLR8, that was delimited in an interval ∼120 kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that O. longistaminata can be exploited to develop lodging-resistant rice lines.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| |
Collapse
|
19
|
Shah L, Yahya M, Shah SMA, Nadeem M, Ali A, Ali A, Wang J, Riaz MW, Rehman S, Wu W, Khan RM, Abbas A, Riaz A, Anis GB, Si H, Jiang H, Ma C. Improving Lodging Resistance: Using Wheat and Rice as Classical Examples. Int J Mol Sci 2019; 20:E4211. [PMID: 31466256 PMCID: PMC6747267 DOI: 10.3390/ijms20174211] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/04/2019] [Accepted: 08/19/2019] [Indexed: 01/07/2023] Open
Abstract
One of the most chronic constraints to crop production is the grain yield reduction near the crop harvest stage by lodging worldwide. This is more prevalent in cereal crops, particularly in wheat and rice. Major factors associated with lodging involve morphological and anatomical traits along with the chemical composition of the stem. These traits have built up the remarkable relationship in wheat and rice genotypes either prone to lodging or displaying lodging resistance. In this review, we have made a comparison of our conceptual perceptions with foregoing published reports and proposed the fundamental controlling techniques that could be practiced to control the devastating effects of lodging stress. The management of lodging stress is, however, reliant on chemical, agronomical, and genetic factors that are reducing the risk of lodging threat in wheat and rice. But, still, there are many questions remain to be answered to elucidate the complex lodging phenomenon, so agronomists, breeders, physiologists, and molecular biologists require further investigation to address this challenging problem.
Collapse
Affiliation(s)
- Liaqat Shah
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Yahya
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Syed Mehar Ali Shah
- Department of Plant Breeding and Genetics, University of Agriculture Peshawar, Peshawar 57000, Pakistan
| | - Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Asif Ali
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Jing Wang
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Waheed Riaz
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Shamsur Rehman
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Weixun Wu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Riaz Muhammad Khan
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Adil Abbas
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Aamir Riaz
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Galal Bakr Anis
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
- Rice Research and Training Center, Field Crops Research Institute, Agriculture Research Center, Kafrelsheikh 33717, Egypt
| | - Hongqi Si
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China.
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| |
Collapse
|