1
|
Lei X, Li H, Li P, Zhang H, Han Z, Yang B, Duan Y, Njeri NS, Yang D, Zheng J, Ma Y, Zhu X, Fang W. Genome-Wide Association Studies of Biluochun Tea Plant Populations in Dongting Mountain and Comprehensive Identification of Candidate Genes Associated with Core Agronomic Traits by Four Analysis Models. Plants (Basel) 2023; 12:3719. [PMID: 37960075 PMCID: PMC10650078 DOI: 10.3390/plants12213719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The elite germplasm resources are key to the beautiful appearance and pleasant flavor of Biluochun tea. We collected and measured the agronomic traits of 95 tea plants to reveal the trait diversity and breeding value of Biluochun tea plant populations. The results revealed that the agronomic traits of Biluochun tea plant populations were diverse and had high breeding value. Additionally, we resequenced these tea plant populations to reveal genetic diversity, population structure, and selection pressure. The Biluochun tea plant populations contained two groups and were least affected by natural selection based on the results of population structure and selection pressure. More importantly, four non-synonymous single nucleotide polymorphisms (nsSNPs) and candidate genes associated with (-)-gallocatechin gallate (GCG), (-)-gallocatechin (GC), and caffeine (CAF) were detected using at least two GWAS models. The results will promote the development and application of molecular markers and the utilization of elite germplasm from Biluochun populations.
Collapse
Affiliation(s)
- Xiaogang Lei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Haoyu Li
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Pingping Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Huan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Bin Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Ndombi Salome Njeri
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Daqiang Yang
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Junhua Zheng
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| |
Collapse
|
2
|
Draga S, Gabelli G, Palumbo F, Barcaccia G. Genome-Wide Datasets of Chicories ( Cichorium intybus L.) for Marker-Assisted Crop Breeding Applications: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:11663. [PMID: 37511422 PMCID: PMC10380310 DOI: 10.3390/ijms241411663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Cichorium intybus L. is the most economically important species of its genus and among the most important of the Asteraceae family. In chicory, many linkage maps have been produced, several sets of mapped and unmapped markers have been developed, and dozens of genes linked to traits of agronomic interest have been investigated. This treasure trove of information, properly cataloged and organized, is of pivotal importance for the development of superior commercial products with valuable agronomic potential in terms of yield and quality, including reduced bitter taste and increased inulin production, as well as resistance or tolerance to pathogens and resilience to environmental stresses. For this reason, a systematic review was conducted based on the scientific literature published in chicory during 1980-2023. Based on the results obtained from the meta-analysis, we created two consensus maps capable of supporting marker-assisted breeding (MAB) and marker-assisted selection (MAS) programs. By taking advantage of the recently released genome of C. intybus, we built a 639 molecular marker-based consensus map collecting all the available mapped and unmapped SNP and SSR loci available for this species. In the following section, after summarizing and discussing all the genes investigated in chicory and related to traits of interest such as reproductive barriers, sesquiterpene lactone biosynthesis, inulin metabolism and stress response, we produced a second map encompassing 64 loci that could be useful for MAS purposes. With the advent of omics technologies, molecular data chaos (namely, the situation where the amount of molecular data is so complex and unmanageable that their use becomes challenging) is becoming far from a negligible issue. In this review, we have therefore tried to contribute by standardizing and organizing the molecular data produced thus far in chicory to facilitate the work of breeders.
Collapse
Affiliation(s)
| | | | - Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (S.D.); (G.G.)
| | - Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (S.D.); (G.G.)
| |
Collapse
|
3
|
Hassan MA, Dahu N, Hongning T, Qian Z, Yueming Y, Yiru L, Shimei W. Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding. Front Plant Sci 2023; 14:1215371. [PMID: 37534289 PMCID: PMC10391551 DOI: 10.3389/fpls.2023.1215371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.
Collapse
Affiliation(s)
- Muhammad A. Hassan
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ni Dahu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tong Hongning
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Qian
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yi Yueming
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Li Yiru
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wang Shimei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| |
Collapse
|
4
|
Barik SR, Moharana A, Pandit E, Behera A, Mishra A, Mohanty SP, Mohapatra S, Sanghamitra P, Meher J, Pani DR, Bhadana VP, Datt S, Sahoo CR, Raj K R R, Pradhan SK. Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches. Int J Mol Sci 2023; 24:10708. [PMID: 37445885 DOI: 10.3390/ijms241310708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 07/15/2023] Open
Abstract
Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC1F1, BC2F1, and BC3F1 generation, respectively. Recurrent parent's genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC3F2 progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.
Collapse
Affiliation(s)
| | - Arpita Moharana
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Elssa Pandit
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, India
| | | | - Ankita Mishra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | | | - Shibani Mohapatra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | | | | | - Dipti Ranjan Pani
- ICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, India
| | - Vijai Pal Bhadana
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834003, India
| | - Shiv Datt
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
| | - Chita Ranjan Sahoo
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Reshmi Raj K R
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
| |
Collapse
|
5
|
Zafer MZ, Tahir MHN, Khan Z, Sajjad M, Gao X, Bakhtavar MA, Waheed U, Siddique M, Geng Z, Ur Rehman S. Genome-Wide Characterization and Sequence Polymorphism Analyses of Glycine max Fibrillin ( FBN) Revealed Its Role in Response to Drought Condition. Genes (Basel) 2023; 14:1188. [PMID: 37372368 DOI: 10.3390/genes14061188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/29/2023] Open
Abstract
The fibrillin (FBN) gene family is widely distributed in all photosynthetic organisms. Members of this gene family are involved in plant growth and development and their response to various biotic and abiotic stress factors. In this study, 16 members of FBN were identified in Glycine max and characterized by using different bioinformatics tools. Phylogenetic analysis classified FBN genes into seven groups. The presence of stress-related cis-elements in the upstream region of GmFBN highlighted their role in tolerance against abiotic stresses. To further decipher the function, physiochemical properties, conserved motifs, chromosomal localization, subcellular localization, and cis-acting regulatory elements were also analyzed. Gene expression analysis based on FPKM values revealed that GmFBNs greatly enhanced soybean drought tolerance and controlled the expression of several genes involved in drought response, except for GmFBN-4, GmFBN-5, GmFBN-6, GmFBN-7 and GmFBN-9. For high throughput genotyping, an SNP-based CAPS marker was also developed for the GmFBN-15 gene. The CAPS marker differentiated soybean genotypes based on the presence of either the GmFBN-15-G or GmFBN-15-A alleles in the CDS region. Association analysis showed that G. max accessions containing the GmFBN-15-A allele at the respective locus showed higher thousand seed weight compared to accessions containing the GmFBN-15-G allele. This research has provided the basic information to further decipher the function of FBN in soybean.
Collapse
Affiliation(s)
- Muhammad Zeshan Zafer
- SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Muhammad Hammad Nadeem Tahir
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Zulqurnain Khan
- SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University, Islamabad (CUI), Park Road, Islamabad 45550, Pakistan
| | - Xiangkuo Gao
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Muhammad Amir Bakhtavar
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Ummara Waheed
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Maria Siddique
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Zhide Geng
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Shoaib Ur Rehman
- SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| |
Collapse
|
6
|
Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
Collapse
Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
| |
Collapse
|
7
|
Park HS, Lee CM, Baek MK, Jeong OY, Kim SM. Application of a Novel Quantitative Trait Locus Combination to Improve Grain Shape without Yield Loss in Rice ( Oryza sativa L. spp. japonica). Plants (Basel) 2023; 12:1513. [PMID: 37050138 PMCID: PMC10097285 DOI: 10.3390/plants12071513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/18/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Grain shape is one of the key factors deciding the yield product and the market value as appearance quality in rice (Oryza sativa L.). The grain shape of japonica cultivars in Korea is quite monotonous because the selection pressure of rice breeding programs works in consideration of consumer preference. In this study, we identified QTLs associated with grain shape to improve the variety of grain shapes in Korean cultivars. QTL analysis revealed that eight QTLs related to five tested traits were detected on chromosomes 2, 5, and 10. Among them, three QTLs-qGL2 (33.9% of PEV for grain length), qGW5 (64.42% for grain width), and qGT10 (49.2% for grain thickness)-were regarded as the main effect QTLs. Using the three QTLs, an ideal QTL combination (qGL2P + qGW5P + qGT10B) could be constructed on the basis of the accumulated QTL effect without yield loss caused by the change in grain shape in the population. In addition, three promising lines with a slender grain type were selected as a breeding resource with a japonica genetic background based on the QTL combination. The application of QTLs detected in this study could improve the grain shape of japonica cultivars without any linkage drag or yield loss.
Collapse
Affiliation(s)
- Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - O-Young Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Suk-Man Kim
- Department of Ecological & Environmental System, Kyungpook National University, Sangju 37224, Republic of Korea
| |
Collapse
|
8
|
Zhao S, Zhang C, Wang L, Luo M, Zhang P, Wang Y, Malik WA, Wang Y, Chen P, Qiu X, Wang C, Lu H, Xiang Y, Liu Y, Ruan J, Qian Q, Zhi H, Chang Y. A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing. J Integr Plant Biol 2023; 65:633-645. [PMID: 36269601 DOI: 10.1111/jipb.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products. Based on this observation, we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing (FBI-seq) using one specific primer, in which foreground genotyping is performed by primer-template perfect annealing (PTPA), while background genotyping employs PTMA. Unlike DNA arrays, multiple PCR, or genome target enrichments, FBI-seq requires little preliminary work for primer design and synthesis, and it is easily adaptable to different foreground genes and species. FBI-seq therefore provides a prolific, robust, and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the post-genomics era.
Collapse
Affiliation(s)
- Sheng Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- 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, 518120, China
| | - Cuicui Zhang
- 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, 518120, China
| | - Liqun Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Minxuan Luo
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- 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, 518120, China
| | - Peng Zhang
- 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, 518120, China
| | - Yue Wang
- 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, 518120, China
| | - Waqar Afzal Malik
- 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, 518120, China
| | - Yue Wang
- 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, 518120, China
| | - Peng 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, 518120, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, 434023, China
| | - Chongrong Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hong 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, 518120, China
| | - Yong Xiang
- 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, 518120, China
| | - Yuwen 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, 518120, China
| | - Jue Ruan
- 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, 518120, China
| | - Qian Qian
- 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, 518120, China
| | - Haijian Zhi
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuxiao Chang
- 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, 518120, China
| |
Collapse
|
9
|
Zaracho N, Reig G, Kalluri N, Arús P, Eduardo I. Inheritance of Fruit Red-Flesh Patterns in Peach. Plants (Basel) 2023; 12:plants12020394. [PMID: 36679108 PMCID: PMC9862646 DOI: 10.3390/plants12020394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 06/01/2023]
Abstract
Fruit color is an important trait in peach from the point of view of consumer preference, nutritional content, and diversification of fruit typologies. Several genes and phenotypes have been described for peach flesh and skin color, and although peach color knowledge has increased in the last few years, some fruit color patterns observed in peach breeding programs have not been carefully described. In this work, we first describe some peach mesocarp color patterns that have not yet been described in a collection of commercial peach cultivars, and we also study the genetic inheritance of the red dots present in the flesh (RDF) and red color around the stone (CAS) in several intra- and interspecific segregating populations for both traits. For RDF, we identified a QTL at the beginning of G5 in two intraspecific populations, and for CAS we identified a major QTL in G4 in both an intraspecific and an interspecific population between almond and peach. Finally, we discuss the interaction between these QTLs and some other genes previously identified in peach, such as dominant blood flesh (DBF), color around the stone (Cs), subacid (D) and the maturity date (MD), and the implications for peach breeding. The results obtained here will help peach germplasm curators and breeders to better characterize their plant materials and to develop an integrated system of molecular markers to select these traits.
Collapse
Affiliation(s)
- Nathalia Zaracho
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Gemma Reig
- Institut de Recerca i Tecnologia Agroalimentaria (IRTA) Fruitcentre, Programa Fructicultura, PCiTAL, Parc Gardeny, 25003 Lleida, Spain
| | - Naveen Kalluri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentaria (IRTA), Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentaria (IRTA), Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| |
Collapse
|
10
|
Koul B, Sharma K, Sehgal V, Yadav D, Mishra M, Bharadwaj C. Chickpea ( Cicer arietinum L.) Biology and Biotechnology: From Domestication to Biofortification and Biopharming. Plants (Basel) 2022; 11:plants11212926. [PMID: 36365379 PMCID: PMC9654780 DOI: 10.3390/plants11212926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 05/13/2023]
Abstract
Chickpea (Cicer arietinum L.), the world's second most consumed legume crop, is cultivated in more than 50 countries around the world. It is a boon for diabetics and is an excellent source of important nutrients such as vitamins A, C, E, K, B1-B3, B5, B6, B9 and minerals (Fe, Zn, Mg and Ca) which all have beneficial effects on human health. By 2050, the world population can cross 9 billion, and in order to feed the teaming millions, chickpea production should also be increased, as it is a healthy alternative to wheat flour and a boon for diabetics. Moreover, it is an important legume that is crucial for food, nutrition, and health security and the livelihood of the small-scale farmers with poor resources, in developing countries. Although marvelous improvement has been made in the development of biotic and abiotic stress-resistant varieties, still there are many lacunae, and to fulfill that, the incorporation of genomic technologies in chickpea breeding (genomics-assisted breeding, high-throughput and precise-phenotyping and implementation of novel breeding strategies) will facilitate the researchers in developing high yielding, climate resilient, water use efficient, salt-tolerant, insect/pathogen resistant varieties, acceptable to farmers, consumers, and industries. This review focuses on the origin and distribution, nutritional profile, genomic studies, and recent updates on crop improvement strategies for combating abiotic and biotic stresses in chickpea.
Collapse
Affiliation(s)
- Bhupendra Koul
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Komal Sharma
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Vrinda Sehgal
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Meerambika Mishra
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi 110012, India
| |
Collapse
|
11
|
Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. Front Plant Sci 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
Collapse
Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
| |
Collapse
|
12
|
Rey-Serra P, Mnejja M, Monfort A. Inheritance of esters and other volatile compounds responsible for the fruity aroma in strawberry. Front Plant Sci 2022; 13:959155. [PMID: 36035685 PMCID: PMC9412188 DOI: 10.3389/fpls.2022.959155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 05/27/2023]
Abstract
Cultivated strawberry, Fragaria × ananassa, has a complex aroma due to the presence of more than 350 volatile organic compounds (VOCs). However, a mixture of only 19 compounds, called Key Volatile Compounds (KVC), can impart the main strawberry aroma. The octoploid nature of the cultivated strawberry species (2n = 8x = 56) adds complexity to the heritance of the accumulation of the volatiles responsible for aroma. An F1 population cross between two breeding parental lines, FC50 and FD54, was phenotyped for aroma by SPME GCMS during six harvests. A total of 58 compounds were identified: 33 esters, nine terpenes, seven aldehydes, four lactones, two furans, one acid, one alkane and one alcohol, of which 16 were KVCs. A total of 179 QTLs were found, and 85 of these were detected in at least three harvests, of which 50 QTLs were considered major (LOD > 4.0) and detected in five or six analyzed harvests. Several clusters of ester QTLs associated with fruity aroma were discovered, such as QTLs for esters that share hexanoate group that were mapped in LG4A (Hexanoate_4A), those that share acetate and octyl groups in LG6A (Acetate_6A and Octyl_6A) or those with the same methyl group in LG7B (Methyl_7B). Different terpene QTLs associated with floral aroma appear grouped in a cluster in LG3C (Terpene_3C). Some of these clusters of QTLs were validated in a second F2 population, a cross of "Camarosa" and "Dover," that was also phenotyped for three years. Selected SNPs from floral and fruity aroma QTLs were tested in a third population, which will most likely be useful for marker-assisted breeding (MAB).
Collapse
Affiliation(s)
- Pol Rey-Serra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Mourad Mnejja
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Amparo Monfort
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| |
Collapse
|
13
|
Somta P, Laosatit K, Yuan X, Chen X. Thirty Years of Mungbean Genome Research: Where Do We Stand and What Have We Learned? Front Plant Sci 2022; 13:944721. [PMID: 35909762 PMCID: PMC9335052 DOI: 10.3389/fpls.2022.944721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Mungbean is a socioeconomically important legume crop in Asia that is currently in high demand by consumers and industries both as dried beans and in plant-based protein foods. Marker-assisted and genomics-assisted breeding are promising approaches to efficiently and rapidly develop new cultivars with improved yield, quality, and resistance to biotic and abiotic stresses. Although mungbean was at the forefront of research at the dawn of the plant genomics era 30 years ago, the crop is a "slow runner" in genome research due to limited genomic resources, especially DNA markers. Significant progress in mungbean genome research was achieved only within the last 10 years, notably after the release of the VC1973A draft reference genome constructed using next-generation sequencing technology, which enabled fast and efficient DNA marker development, gene mapping, and identification of candidate genes for complex traits. Resistance to biotic stresses has dominated mungbean genome research to date; however, research is on the rise. In this study, we provide an overview of the past progress and current status of mungbean genomics research. We also discuss and evaluate some research results to provide a better understanding of mungbean genomics.
Collapse
Affiliation(s)
- Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
14
|
Baye W, Xie Q, Xie P. Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:2405. [PMID: 35269548 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
Collapse
|
15
|
Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
Collapse
|
16
|
Ravi S, Campagna G, Della Lucia MC, Broccanello C, Bertoldo G, Chiodi C, Maretto L, Moro M, Eslami AS, Srinivasan S, Squartini A, Concheri G, Stevanato P. SNP Alleles Associated With Low Bolting Tendency in Sugar Beet. Front Plant Sci 2021; 12:693285. [PMID: 34322145 PMCID: PMC8311237 DOI: 10.3389/fpls.2021.693285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet (Beta vulgaris L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study. An elaborate 3-year field trial comprising 13 sugar beet lines identified L14 as the one exhibiting the lowest bolting tendency along with an increased survival rate after autumnal sowing. For SNP discovery following phenotyping, contrasting phenotypes of 24 non-bolting and 15 bolting plants of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq). An association model was established with a set of 10,924 RAD-based single nucleotide polymorphism (SNP) markers. The allelic status of the most significantly associated SNPs ranked based on their differential allelic status between contrasting phenotypes (p < 0.01) was confirmed on three different validation datasets comprising diverse sugar beet lines and varieties adopting a range of SNP detection technologies. This study has led to the identification of SNP_36780842 and SNP_48607347 linked to low bolting tendency and can be used for marker-assisted breeding and selection in sugar beet.
Collapse
Affiliation(s)
- Samathmika Ravi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Giovanni Campagna
- Cooperativa Produttori Agricoli Società Cooperativa Agricola (COPROB), Minerbio, Italy
| | - Maria Cristina Della Lucia
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Claudia Chiodi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Laura Maretto
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Matteo Moro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Azam Sadat Eslami
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | | | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| |
Collapse
|
17
|
Wu J, Yu R, Wang H, Zhou C, Huang S, Jiao H, Yu S, Nie X, Wang Q, Liu S, Weining S, Singh RP, Bhavani S, Kang Z, Han D, Zeng Q. A large-scale genomic association analysis identifies the candidate causal genes conferring stripe rust resistance under multiple field environments. Plant Biotechnol J 2021; 19:177-191. [PMID: 32677132 PMCID: PMC7769225 DOI: 10.1111/pbi.13452] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 05/02/2023]
Abstract
The incorporation of resistance genes into wheat commercial varieties is the ideal strategy to combat stripe or yellow rust (YR). In a search for novel resistance genes, we performed a large-scale genomic association analysis with high-density 660K single nucleotide polymorphism (SNP) arrays to determine the genetic components of YR resistance in 411 spring wheat lines. Following quality control, 371 972 SNPs were screened, covering over 50% of the high-confidence annotated gene space. Nineteen stable genomic regions harbouring 292 significant SNPs were associated with adult-plant YR resistance across nine environments. Of these, 14 SNPs were localized in the proximity of known loci widely used in breeding. Obvious candidate SNP variants were identified in certain confidence intervals, such as the cloned gene Yr18 and the major locus on chromosome 2BL, despite a large extent of linkage disequilibrium. The number of causal SNP variants was refined using an independent validation panel and consideration of the estimated functional importance of each nucleotide polymorphism. Interestingly, four natural polymorphisms causing amino acid changes in the gene TraesCS2B01G513100 that encodes a serine/threonine protein kinase (STPK) were significantly involved in YR responses. Gene expression and mutation analysis confirmed that STPK played an important role in YR resistance. PCR markers were developed to identify the favourable TraesCS2B01G513100 haplotype for marker-assisted breeding. These results demonstrate that high-resolution SNP-based GWAS enables the rapid identification of putative resistance genes and can be used to improve the efficiency of marker-assisted selection in wheat disease resistance breeding.
Collapse
Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Cai'e Zhou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Hanxuan Jiao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Song Weining
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT)TexcocoEstado de MexicoMexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT)TexcocoEstado de MexicoMexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| |
Collapse
|
18
|
Ruiz-García L, Gago P, Martínez-Mora C, Santiago JL, Fernádez-López DJ, Martínez MDC, Boso S. Evaluation and Pre-selection of New Grapevine Genotypes Resistant to Downy and Powdery Mildew, Obtained by Cross-Breeding Programs in Spain. Front Plant Sci 2021; 12:674510. [PMID: 34956246 PMCID: PMC8703198 DOI: 10.3389/fpls.2021.674510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 11/22/2021] [Indexed: 05/08/2023]
Abstract
The need to develop an environmentally friendly, sustainable viticulture model has led to numerous grapevine improvement programmes aiming to increase resistance to downy and powdery mildew. The success of such programmes relies on the availability of protocols that can quantify the resistance/susceptibility of new genotypes, and on the existence of molecular markers of resistance loci that can aid in the selection process. The present work assesses the degree of phenotypic resistance/susceptibility to downy and powdery mildew of 28 new genotypes obtained from crosses between "Monastrell" and "Regent." Three genotypes showed strong combined resistance, making them good candidates for future crosses with other sources of resistance to these diseases (pyramiding). In general, laboratory and glasshouse assessments of resistance at the phenotype level agreed with the resistance expected from the presence of resistance-associated alleles of simple sequence repeat (SSR) markers for the loci Rpv3 and Ren3 (inherited from "Regent"), confirming their usefulness as indicators of likely resistance to downy and powdery mildew, respectively, particularly so for downy mildew.
Collapse
Affiliation(s)
- Leonor Ruiz-García
- Department of Biotechnology, Genomics and Plant Breeding, Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Murcia, Spain
| | - Pilar Gago
- Department of Viticulture and Forestry, Misión Biológica de Galicia (Consejo Superior de Investigaciones Científicas, CSIC), Salcedo, Spain
| | - Celia Martínez-Mora
- Department of Biotechnology, Genomics and Plant Breeding, Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Murcia, Spain
| | - José Luis Santiago
- Department of Viticulture and Forestry, Misión Biológica de Galicia (Consejo Superior de Investigaciones Científicas, CSIC), Salcedo, Spain
| | - Diego J. Fernádez-López
- Department of Biotechnology, Genomics and Plant Breeding, Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Murcia, Spain
| | - María del Carmen Martínez
- Department of Viticulture and Forestry, Misión Biológica de Galicia (Consejo Superior de Investigaciones Científicas, CSIC), Salcedo, Spain
| | - Susana Boso
- Department of Viticulture and Forestry, Misión Biológica de Galicia (Consejo Superior de Investigaciones Científicas, CSIC), Salcedo, Spain
- *Correspondence: Susana Boso,
| |
Collapse
|
19
|
Mohapatra S, Panda AK, Bastia AK, Mukherjee AK, Sanghamitra P, Meher J, Mohanty SP, Pradhan SK. Development of Submergence-Tolerant, Bacterial Blight-Resistant, and High-Yielding Near Isogenic Lines of Popular Variety, 'Swarna' Through Marker-Assisted Breeding Approach. Front Plant Sci 2021; 12:672618. [PMID: 34386025 PMCID: PMC8353458 DOI: 10.3389/fpls.2021.672618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 05/13/2023]
Abstract
The rice variety 'Swarna' is highly popular in the eastern region of India. The farmers of eastern India cultivate mainly rainfed rice and face the adverse effects of climate change very frequently. Rice production in this region is not stable. Swarna variety is highly susceptible to bacterial blight (BB) disease and flash floods, which cause a heavy reduction in the yield. Transfer of five target genes/QTLs was targeted into the variety, Swarna by adopting marker-assisted backcross breeding approach. Direct markers for Sub1A, OsSPL14, and SCM2 QTLs and closely linked markers for xa5 and Xa21 BB resistance genes were screened in the backcross progenies. Swarna-Sub1, CR Dhan 800, and Swarna-Habataki near-isogenic lines (NILs) were used as donor parents in the breeding program. True multiple F1 plants were identified for backcrossing, and 796 BC1F1 seeds were generated. Foreground selection detected all the five target genes in six progenies in BC1F1 generation. The progeny containing all the target genes and more similar with the recipient parent was backcrossed, and a total of 446 BC2F1 seeds were produced. Foreground screening detected four BC2F1 plants carrying the five target genes. A total of 2,145 BC2F2 seeds were obtained from the best BC2F1 progeny. Screening of the progenies resulted in one plant with all five desirable genes, three plants with four, and another three progenies carrying three genes in homozygous conditions. The pyramided lines showed higher BB resistance and submergence tolerance than the recipient parent, Swarna. Culm strength of the pyramided lines showed higher breaking force than the recipient parent, Swarna. The pyramided line, SSBY-16-68-69 yielded the highest grain yield of 7.52 t/ha followed by the lines SSBY-16-68-511 (7.34 t/ha) and SSBY-16-68-1633 (7.02 t/ha). The best-pyramided line showed a yield advantage of 18% over the recipient parent and 6.8% over the yield component donor parent. Seven pyramided lines showed higher yield than the recipient parent, while five lines were better yielders than the yield component donor parent. The pyramided line SSBY-16-68-69 produced 365 grains/panicle, while the recipient had 152. The main morphologic and grain quality features of the recipient parent were retained in the pyramided lines.
Collapse
Affiliation(s)
| | - Alok Kumar Panda
- School of Applied Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | | | | | | | | | | | - Sharat Kumar Pradhan
- ICAR—National Rice Research Institute, Cuttack, India
- *Correspondence: Sharat Kumar Pradhan
| |
Collapse
|
20
|
Li N, Yu C, Yin Y, Gao S, Wang F, Jiao C, Yao M. Pepper Crop Improvement Against Cucumber Mosaic Virus (CMV): A Review. Front Plant Sci 2020; 11:598798. [PMID: 33362830 PMCID: PMC7758397 DOI: 10.3389/fpls.2020.598798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Cucumber mosaic virus (CMV) is a prevalent virus affecting the quality and yield of pepper, resulting in yield losses of greater than 80% during severe local epidemics. Cultural practices and the heavy use of agrochemicals are the most common control measures for CMV. Sources of resistance provide a practical reference and a basis for breeding for CMV resistance. Genetic factors underlying CMV resistance have been studied and advanced breeding lines and cultivars with improved resistance have been developed by traditional breeding methods. Additionally, QTLs or genes for CMV resistance have been identified and can be utilized for marker-assisted resistance breeding. This review focuses on status and prospect of CMV against different virus strains, host resistance, and its applied genetics. With the advent of novel technologies, more useful markers and precise approaches can facilitate the progress for improving CMV resistance in Capsicum.
Collapse
Affiliation(s)
| | | | | | | | | | - Chunhai Jiao
- Hubei Key Laboratory of Vegetable Germplasm Innovation and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Minghua Yao
- Hubei Key Laboratory of Vegetable Germplasm Innovation and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
21
|
Abebe AM, Choi J, Kim Y, Oh CS, Yeam I, Nou IS, Lee JM. Development of diagnostic molecular markers for marker-assisted breeding against bacterial wilt in tomato. Breed Sci 2020; 70:462-473. [PMID: 32968349 PMCID: PMC7495205 DOI: 10.1270/jsbbs.20027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Bacterial wilt, caused by the Ralstonia pseudosolanacearum species complex, is an important vascular disease that limits tomato production in tropical and subtropical regions. Two major quantitative trait loci (QTL) of bacterial wilt resistance on chromosome 6 (Bwr-6) and 12 (Bwr-12) were previously identified in Solanum lycopersicum 'Hawaii 7996'; however, marker-assisted breeding for bacterial wilt resistance is not well established. To dissect the QTL, six cleaved amplified polymorphic sites (CAPS) and derived CAPS (dCAPS) markers within the Bwr-6 region and one dCAPS marker near Bwr-12 were developed, and resistance levels in 117 tomato cultivars were evaluated. Two markers, RsR6-5 on chromosome 6 and RsR12-1 on chromosome 12, were selected based on the genotypic and phenotypic analysis. The combination of RsR6-5 and RsR12-1 effectively distinguishes resistant and susceptible cultivars. Furthermore, the efficiency of the two markers was validated in the F3 generation derived from the F2 population between E6203 (susceptible) and Hawaii 7998 (resistant). Resistant alleles at both loci led to the resistance to bacterial wilt. These markers will facilitate marker-assisted breeding of tomato resistant to bacterial wilt.
Collapse
Affiliation(s)
- Alebel Mekuriaw Abebe
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| | - Jinwoo Choi
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| | - Youngjun Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, Gyeonggi-do 17104, South Korea
| | - Inhwa Yeam
- Department of Horticulture and Breeding, Andong National University, Andong, Gyeongbuk, 36729, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 57922, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| |
Collapse
|
22
|
Sun C, Dong Z, Zhao L, Ren Y, Zhang N, Chen F. The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat. Plant Biotechnol J 2020; 18:1354-1360. [PMID: 32065714 PMCID: PMC7206996 DOI: 10.1111/pbi.13361] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/22/2020] [Accepted: 02/01/2020] [Indexed: 05/11/2023]
Abstract
The rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCR-based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.
Collapse
Affiliation(s)
- Congwei Sun
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Zhongdong Dong
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| |
Collapse
|
23
|
Sasai R, Tabuchi H, Shirasawa K, Kishimoto K, Sato S, Okada Y, Kuramoto A, Kobayashi A, Isobe S, Tahara M, Monden Y. Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. DNA Res 2020; 26:399-409. [PMID: 31377774 PMCID: PMC6796513 DOI: 10.1093/dnares/dsz018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.
Collapse
Affiliation(s)
- Rumi Sasai
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Hiroaki Tabuchi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | | | - Kazuki Kishimoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Shusei Sato
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yoshihiro Okada
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | - Akihide Kuramoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, Japan
| | - Akira Kobayashi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| |
Collapse
|
24
|
Sargolzaei M, Maddalena G, Bitsadze N, Maghradze D, Bianco PA, Failla O, Toffolatti SL, De Lorenzis G. Rpv29, Rpv30 and Rpv31: Three Novel Genomic Loci Associated With Resistance to Plasmopara viticola in Vitis vinifera. Front Plant Sci 2020; 11:562432. [PMID: 33163011 PMCID: PMC7583455 DOI: 10.3389/fpls.2020.562432] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/17/2020] [Indexed: 05/21/2023]
Abstract
Plasmopara viticola (Berk. et Curt.) Berl. and de Toni, the agent of downy mildew, is one of the most important pathogens of European grapevine (Vitis vinifera L.). Extensive evaluation of cultivated grapevine germplasm has highlighted the existence of resistant phenotypes in the Georgian (Southern Caucasus) germplasm. Resistance is shown as a reduction in disease severity. Unraveling the genetic architecture of grapevine response to P. viticola infection is crucial to develop resistant varieties and reduce the impact of disease management. The aim of this work was to apply a genome-wide association (GWA) approach to a panel of Georgian-derived accessions phenotyped for P. viticola susceptibility and genotyped with Vitis18kSNP chip array. GWA identified three highly significant novel loci on chromosomes 14 (Rpv29), 3 (Rpv30) and 16 (Rpv31) associated with a low level of pathogen sporulation. Rpv29, Rpv30, and Rpv31 loci appeared to be associated with plant defense genes against biotic stresses, such as genes involved in pathogen recognition and signal transduction. This study provides the first evidence of resistant loci against P. viticola in V. vinifera germplasm, and identifies potential target genes for breeding P. viticola resistant grapevine cultivars.
Collapse
Affiliation(s)
- Maryam Sargolzaei
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Giuliana Maddalena
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Nana Bitsadze
- Department of Agriculture and Life Sciences, Agricultural University of Georgia, Tbilisi, Georgia
| | - David Maghradze
- Faculty of Viticulture and Winemaking, Caucasus International University, Tbilisi, Georgia
- National Wine Agency of Georgia, Tbilisi, Georgia
| | - Piero Attilio Bianco
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Osvaldo Failla
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Silvia Laura Toffolatti
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
- *Correspondence: Gabriella De Lorenzis,
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
- Silvia Laura Toffolatti,
| |
Collapse
|
25
|
Pradhan S, Babar MA, Robbins K, Bai G, Mason RE, Khan J, Shahi D, Avci M, Guo J, Maksud Hossain M, Bhatta M, Mergoum M, Asseng S, Amand PS, Gezan S, Baik BK, Blount A, Bernardo A. Understanding the Genetic Basis of Spike Fertility to Improve Grain Number, Harvest Index, and Grain Yield in Wheat Under High Temperature Stress Environments. Front Plant Sci 2019; 10:1481. [PMID: 31850009 PMCID: PMC6895025 DOI: 10.3389/fpls.2019.01481] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/25/2019] [Indexed: 05/22/2023]
Abstract
Moderate heat stress accompanied by short episodes of extreme heat during the post-anthesis stage is common in most US wheat growing areas and causes substantial yield losses. Sink strength (grain number) is a key yield limiting factor in modern wheat varieties. Increasing spike fertility (SF) and improving the partitioning of assimilates can optimize sink strength which is essential to improve wheat yield potential under a hot and humid environment. A genome-wide association study (GWAS) allows identification of novel quantitative trait loci (QTLs) associated with SF and other partitioning traits that can assist in marker assisted breeding. In this study, GWAS was performed on a soft wheat association mapping panel (SWAMP) comprised of 236 elite lines using 27,466 single nucleotide polymorphisms (SNPs). The panel was phenotyped in two heat stress locations over 3 years. GWAS identified 109 significant marker-trait associations (MTAs) (p ≤ 9.99 x 10-5) related to eight phenotypic traits including SF (a major component of grain number) and spike harvest index (SHI, a major component of grain weight). MTAs detected on chromosomes 1B, 3A, 3B, and 5A were associated with multiple traits and are potentially important targets for selection. More than half of the significant MTAs (60 out of 109) were found in genes encoding different types of proteins related to metabolism, disease, and abiotic stress including heat stress. These MTAs could be potential targets for further validation study and may be used in marker-assisted breeding for improving wheat grain yield under post-anthesis heat stress conditions. This is the first study to identify novel QTLs associated with SF and SHI which represent the major components of grain number and grain weight, respectively, in wheat.
Collapse
Affiliation(s)
- Sumit Pradhan
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Md Ali Babar
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Kelly Robbins
- School of Integrative Plant Science, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | - Richard Esten Mason
- Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Jahangir Khan
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Dipendra Shahi
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Muhsin Avci
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Jia Guo
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | | | - Madhav Bhatta
- Department of Agronomy, University of Wisconsin, Madison, WI, United States
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Senthold Asseng
- Agricultural and Biological Engineering, University of Florida, Gainesville, FL, United States
| | | | - Salvador Gezan
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | | | - Ann Blount
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Amy Bernardo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| |
Collapse
|
26
|
Patella A, Palumbo F, Galla G, Barcaccia G. The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce ( Lactuca sativa L.). Genes (Basel) 2019; 10:E916. [PMID: 31717592 PMCID: PMC6895879 DOI: 10.3390/genes10110916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/26/2022] Open
Abstract
The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species' spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce.
Collapse
Affiliation(s)
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro PD, Italy; (A.P.); (G.G.); (G.B.)
| | | | | |
Collapse
|
27
|
Karikari B, Chen S, Xiao Y, Chang F, Zhou Y, Kong J, Bhat JA, Zhao T. Utilization of Interspecific High-Density Genetic Map of RIL Population for the QTL Detection and Candidate Gene Mining for 100-Seed Weight in Soybean. Front Plant Sci 2019; 10:1001. [PMID: 31552060 PMCID: PMC6737081 DOI: 10.3389/fpls.2019.01001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/17/2019] [Indexed: 05/26/2023]
Abstract
Seed-weight is one of the most important traits determining soybean yield. Hence, it is prerequisite to have detailed understanding of the genetic basis regulating seed-weight for the development of improved cultivars. In this regard, the present study used high-density interspecific linkage map of NJIR4P recombinant inbred population evaluated in four different environments to detect stable Quantitative trait loci (QTLs) as well as mine candidate genes for 100-seed weight. In total, 19 QTLs distributed on 12 chromosomes were identified in all individual environments plus combined environment, out of which seven were novel and eight are stable identified in more than one environment. However, all the novel QTLs were minor (R 2 < 10%). The remaining 12 QTLs detected in this study were co-localized with the earlier reported QTLs with narrow genomic regions, and out of these only 2 QTLs were major (R 2 > 10%) viz., qSW-17-1 and qSW-17-4. Beneficial alleles of all identified QTLs were derived from cultivated soybean parent (Nannong493-1). Based on Protein ANalysis THrough Evolutionary Relationships, gene annotation information, and literature search, 29 genes within 5 stable QTLs were predicted to be possible candidate genes that might regulate seed-weight/size in soybean. However, it needs further validation to confirm their role in seed development. In conclusion, the present study provides better understanding of trait genetics and candidate gene information through the use high-density inter-specific bin map, and also revealed considerable scope for genetic improvement of 100-seed weight in soybean using marker-assisted breeding.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
28
|
Zini E, Dolzani C, Stefanini M, Gratl V, Bettinelli P, Nicolini D, Betta G, Dorigatti C, Velasco R, Letschka T, Vezzulli S. R-Loci Arrangement Versus Downy and Powdery Mildew Resistance Level: A Vitis Hybrid Survey. Int J Mol Sci 2019; 20:ijms20143526. [PMID: 31323823 PMCID: PMC6679420 DOI: 10.3390/ijms20143526] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
For the viticulture of the future, it will be an essential prerequisite to manage grapevine diseases with fewer chemical inputs. The development and the deployment of novel mildew resistant varieties are considered one of the most promising strategies towards a sustainable viticulture. In this regard, a collection of 102 accessions derived from crossing Vitis hybrids with V. vinifera varieties was studied. In addition to the true-to-type analysis, an exhaustive genetic characterization was carried out at the 11 reliable mildew resistance (R) loci available in the literature to date. Our findings highlight the pyramiding of R-loci against downy mildew in 15.7% and against powdery mildew in 39.2% of the total accessions. The genetic analysis was coupled with a three-year evaluation of disease symptoms in an untreated field in order to assess the impact of the R-loci arrangement on the disease resistance degree at leaf and bunch level. Overall, our results strongly suggest that R-loci pyramiding does not necessarily mean to increase the overall disease resistance, but it guarantees the presence of further barriers in case of pathogens overcoming the first. Moreover, our survey allows the discovery of new mildew resistance sources useful for novel QTL identifications towards marker-assisted breeding.
Collapse
Affiliation(s)
- Elena Zini
- Laimburg Research Centre, Laimburg 6, 39052 Vadena (BZ), Italy
| | - Chiara Dolzani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Verena Gratl
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | | | - Daniela Nicolini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Giulia Betta
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Cinzia Dorigatti
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Thomas Letschka
- Laimburg Research Centre, Laimburg 6, 39052 Vadena (BZ), Italy.
| | - Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
| |
Collapse
|
29
|
Ali J, Aslam UM, Tariq R, Murugaiyan V, Schnable PS, Li D, Marfori-Nazarea CM, Hernandez JE, Arif M, Xu J, Li Z. Exploiting the Genomic Diversity of Rice ( Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations. Front Plant Sci 2018; 9:849. [PMID: 29988489 PMCID: PMC6024854 DOI: 10.3389/fpls.2018.00849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/31/2018] [Indexed: 05/24/2023]
Abstract
This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ∼943.4 million raw reads, out of which ∼881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1-4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.
Collapse
Affiliation(s)
- Jauhar Ali
- International Rice Research Institute, Los Baños, Philippines
| | - Umair M. Aslam
- International Rice Research Institute, Los Baños, Philippines
- Institute of Crop Science, University of the Philippines Los Baños, Los Baños, Philippines
| | - Rida Tariq
- International Rice Research Institute, Los Baños, Philippines
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Patrick S. Schnable
- Data2Bio, LLC, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Delin Li
- Data2Bio, LLC, Ames, IA, United States
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Corinne M. Marfori-Nazarea
- International Rice Research Institute, Los Baños, Philippines
- Institute of Crop Science, University of the Philippines Los Baños, Los Baños, Philippines
| | - Jose E. Hernandez
- Institute of Crop Science, University of the Philippines Los Baños, Los Baños, Philippines
| | - Muhammad Arif
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jianlong Xu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
30
|
Wang B, Zhuang Z, Zhang Z, Draye X, Shuang LS, Shehzad T, Lubbers EL, Jones D, May OL, Paterson AH, Chee PW. Advanced Backcross QTL Analysis of Fiber Strength and Fineness in a Cross between Gossypium hirsutum and G. mustelinum. Front Plant Sci 2017; 8:1848. [PMID: 29118778 PMCID: PMC5661169 DOI: 10.3389/fpls.2017.01848] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 10/10/2017] [Indexed: 05/18/2023]
Abstract
The molecular genetic basis of cotton fiber strength and fineness in crosses between Gossypium mustelinum and Gossypium hirsutum (Upland cotton) was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. The BC3F2 families were genotyped with simple sequence repeat markers from a G. hirsutum by G. mustelinum linkage map, and the three generations of BC3-derived families were phenotyped for fiber strength (STR) and fineness (Micronaire, MIC). A total of 42 quantitative trait loci (QTLs) were identified through one-way analysis of variance, including 15 QTLs for STR and 27 for MIC, with the percentage of variance explained by individual loci averaging 13.86 and 14.06%, respectively. Eighteen of the 42 QTLs were detected at least twice near the same markers in different generations/families or near linked markers in the same family, and 28 of the 42 QTLs were identified in both mixed model-based composite interval mapping and one-way variance analyses. Alleles from G. mustelinum increased STR for eight of 15 and reduced MIC for 15 of 27 QTLs. Significant among-family genotypic effects (P < 0.001) were detected in 13 and 10 loci for STR and MIC respectively, and five loci showed significant (P < 0.001) genotype × family interaction for MIC. These results support the hypothesis that fiber quality improvement for Upland cotton could be realized by introgressing G. mustelinum alleles although complexities due to the different effects of genetic background on introgressed chromatin might be faced. Building on prior work with G. barbadense, G. tomentosum, and G. darwinii, QTL mapping involving introgression of G. mustelinum alleles offers new allelic variation to Upland cotton germplasm.
Collapse
Affiliation(s)
- Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Zhimin Zhuang
- School of Life Sciences, Nantong University, Nantong, China
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Zhengsheng Zhang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xavier Draye
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Lan-Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Edward L. Lubbers
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Don Jones
- Agricultural Research Division, Cotton Incorporated, Cary, NC, United States
| | - O. Lloyd May
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Peng W. Chee
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, United States
| |
Collapse
|
31
|
Rahman MU, Khan AQ, Rahmat Z, Iqbal MA, Zafar Y. Genetics and Genomics of Cotton Leaf Curl Disease, Its Viral Causal Agents and Whitefly Vector: A Way Forward to Sustain Cotton Fiber Security. Front Plant Sci 2017; 8:1157. [PMID: 28725230 PMCID: PMC5495822 DOI: 10.3389/fpls.2017.01157] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc., and practicing mixed type farming system have further exaggerated the situation by adding synergy to the evolution of new viral strains and vectors. Efforts to control this disease using host plant resistance remained successful using two gene based-resistance that was broken by the evolution of new resistance breaking strain called Burewala virus. Development of transgenic cotton using both pathogen and non-pathogenic derived approaches are in progress. In future, screening for new forms of host resistance, use of DNA markers for the rapid incorporation of resistance into adapted cultivars overlaid with transgenics and using genome editing by CRISPR/Cas system would be instrumental in adding multiple layers of defense to control the disease-thus cotton fiber production will be sustained.
Collapse
Affiliation(s)
- Mehboob-ur- Rahman
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Ali Q. Khan
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Zainab Rahmat
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Muhammad A. Iqbal
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Yusuf Zafar
- Pakistan Agricultural Research CouncilIslamabad, Pakistan
| |
Collapse
|
32
|
Abstract
Salt stress reduces land and water productivity and contributes to poverty and food insecurity. Increased salinization caused by human practices and climate change is progressively reducing agriculture productivity despite escalating calls for more food. Plant responses to salt stress are well understood, involving numerous critical processes that are each controlled by multiple genes. Knowledge of the critical mechanisms controlling salt uptake and exclusion from functioning tissues, signaling of salt stress, and the arsenal of protective metabolites is advancing. However, little progress has been made in developing salt-tolerant varieties of crop species using standard (but slow) breeding approaches. The genetic diversity available within cultivated crops and their wild relatives provides rich sources for trait and gene discovery that has yet to be sufficiently utilized. Transforming this knowledge into modern approaches using genomics and molecular tools for precision breeding will accelerate the development of tolerant cultivars and help sustain food production.
Collapse
Affiliation(s)
- Abdelbagi M Ismail
- Genetics and Biotechnology Division, International Rice Research Institute, Manila 1301, Philippines;
| | - Tomoaki Horie
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan;
| |
Collapse
|
33
|
Dhakal R, Chai C, Karan R, Windham GL, Williams WP, Subudhi PK. Expression Profiling Coupled with In-silico Mapping Identifies Candidate Genes for Reducing Aflatoxin Accumulation in Maize. Front Plant Sci 2017; 8:503. [PMID: 28428796 PMCID: PMC5382453 DOI: 10.3389/fpls.2017.00503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/22/2017] [Indexed: 05/31/2023]
Abstract
Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A. flavus infection and map these clones onto the corn genome by in-silico mapping. A total of 267 unigenes were identified and majority of genes were related to metabolism, stress response, and disease resistance. Based on the reverse northern hybridization experiment, 26 DEGs were selected for semi-quantitative RT-PCR analysis in seven inbreds with variable resistance to aflatoxin accumulation at two time points after A. flavus inoculation. Most of these genes were highly expressed in resistant inbreds. Quantitative RT-PCR analysis validated upregulation of PR-4, DEAD-box RNA helicase, and leucine rich repeat family protein in resistant inbreds. Fifty-six unigenes, which were placed on linkage map through in-silico mapping, overlapped the QTL regions for resistance to aflatoxin accumulation identified in a mapping population derived from the cross between B73 and Mp715. Since majority of these mapped genes were related to disease resistance, stress response, and metabolism, these should be ideal candidates to investigate host pathogen interaction and to reduce aflatoxin accumulation in maize.
Collapse
Affiliation(s)
- Ramesh Dhakal
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural CenterBaton Rouge, LA, USA
| | - Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural CenterBaton Rouge, LA, USA
| | - Ratna Karan
- Department of Agronomy, University of FloridaGainesville, FL, USA
| | - Gary L. Windham
- USDA-ARS Corn Host Plant Resistance Research UnitMississippi State, MS, USA
| | | | - Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural CenterBaton Rouge, LA, USA
| |
Collapse
|
34
|
Shivhare R, Lata C. Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet. Front Plant Sci 2017; 7:2069. [PMID: 28167949 PMCID: PMC5253385 DOI: 10.3389/fpls.2016.02069] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/27/2016] [Indexed: 05/05/2023]
Abstract
Pearl millet is one of the most important small-grained C4 Panicoid crops with a large genome size (∼2352 Mb), short life cycle and outbreeding nature. It is highly resilient to areas with scanty rain and high temperature. Pearl millet is a nutritionally superior staple crop for people inhabiting hot, drought-prone arid and semi-arid regions of South Asia and Africa where it is widely grown and used for food, hay, silage, bird feed, building material, and fuel. Having excellent nutrient composition and exceptional buffering capacity against variable climatic conditions and pathogen attack makes pearl millet a wonderful model crop for stress tolerance studies. Pearl millet germplasm show a large range of genotypic and phenotypic variations including tolerance to abiotic and biotic stresses. Conventional breeding for enhancing abiotic and biotic stress resistance in pearl millet have met with considerable success, however, in last few years various novel approaches including functional genomics and molecular breeding have been attempted in this crop for augmenting yield under adverse environmental conditions, and there is still a lot of scope for further improvement using genomic tools. Discovery and use of various DNA-based markers such as EST-SSRs, DArT, CISP, and SSCP-SNP in pearl millet not only help in determining population structure and genetic diversity but also prove to be important for developing strategies for crop improvement at a faster rate and greater precision. Molecular marker-based genetic linkage maps and identification of genomic regions determining yield under abiotic stresses particularly terminal drought have paved way for marker-assisted selection and breeding of pearl millet cultivars. Reference collections and marker-assisted backcrossing have also been used to improve biotic stress resistance in pearl millet specifically to downy mildew. Whole genome sequencing of pearl millet genome will give new insights for processing of functional genes and assist in crop improvement programs through molecular breeding approaches. This review thus summarizes the exploration of pearl millet genetic and genomic resources for improving abiotic and biotic stress resistance and development of cultivars superior in stress tolerance.
Collapse
Affiliation(s)
- Radha Shivhare
- National Botanical Research Institute (CSIR)Lucknow, India
- Academy of Scientific and Innovative ResearchNew Delhi, India
| | - Charu Lata
- National Botanical Research Institute (CSIR)Lucknow, India
- Academy of Scientific and Innovative ResearchNew Delhi, India
| |
Collapse
|
35
|
Zhai S, Xia X, He Z. Carotenoids in Staple Cereals: Metabolism, Regulation, and Genetic Manipulation. Front Plant Sci 2016; 7:1197. [PMID: 27559339 PMCID: PMC4978713 DOI: 10.3389/fpls.2016.01197] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/27/2016] [Indexed: 05/02/2023]
Abstract
Carotenoids play a critical role in animal and human health. Animals and humans are unable to synthesize carotenoids de novo, and therefore rely upon diet as sources of these compounds. However, major staple cereals often contain only small amounts of carotenoids in their grains. Consequently, there is considerable interest in genetic manipulation of carotenoid content in cereal grain. In this review, we focus on carotenoid metabolism and regulation in non-green plant tissues, as well as genetic manipulation in staple cereals such as rice, maize, and wheat. Significant progress has been made in three aspects: (1) seven carotenogenes play vital roles in carotenoid regulation in non-green plant tissues, including 1-deoxyxylulose-5-phosphate synthase influencing isoprenoid precursor supply, phytoene synthase, β-cyclase, and ε-cyclase controlling biosynthesis, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase and carotenoid cleavage dioxygenases responsible for degradation, and orange gene conditioning sequestration sink; (2) provitamin A-biofortified crops, such as rice and maize, were developed by either metabolic engineering or marker-assisted breeding; (3) quantitative trait loci for carotenoid content on chromosomes 3B, 7A, and 7B were consistently identified, eight carotenogenes including 23 loci were detected, and 10 gene-specific markers for carotenoid accumulation were developed and applied in wheat improvement. A comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops will be beneficial in improving our precision in improving carotenoid contents. Genomic selection and gene editing are emerging as transformative technologies for provitamin A biofortification.
Collapse
Affiliation(s)
- Shengnan Zhai
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center, Chinese Academy of Agricultural SciencesBeijing, China
| |
Collapse
|
36
|
Boukar O, Fatokun CA, Huynh BL, Roberts PA, Close TJ. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives. Front Plant Sci 2016; 7:757. [PMID: 27375632 PMCID: PMC4891349 DOI: 10.3389/fpls.2016.00757] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/17/2016] [Indexed: 05/07/2023]
Abstract
Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA.
Collapse
Affiliation(s)
- Ousmane Boukar
- Cowpea Breeding, International Institute of Tropical AgricultureKano, Nigeria
- *Correspondence: Ousmane Boukar
| | | | - Bao-Lam Huynh
- Department of Nematology, University of California, RiversideRiverside, CA, USA
| | - Philip A. Roberts
- Department of Nematology, University of California, RiversideRiverside, CA, USA
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, RiversideRiverside, CA, USA
| |
Collapse
|
37
|
Prince SJ, Beena R, Gomez SM, Senthivel S, Babu RC. Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments. Rice (N Y) 2015; 8:53. [PMID: 26206756 PMCID: PMC4513014 DOI: 10.1186/s12284-015-0053-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 05/22/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB. RESULTS Recombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index. CONCLUSION Three QTL regions on chromosome 1 (RM8085), chromosome 4 (I12S), and chromosome 6 (RM6836) harbor significant additive QTLs for various physiological and yield traits under drought stress. The similar chromosomal region on 4 and 6 were found to harbor QTLs for canopy temperature and leaf drying under drought stress conditions. Thus, the identified large effect yield QTLs could be introgressed to develop rice lines with stable yields under varying natural drought stress predominant in TPEs.
Collapse
Affiliation(s)
- Silvas J Prince
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| | - R Beena
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| | - S Michael Gomez
- International Center for Tropical Agriculture (CIAT), Colombia, 6713 Colombia
| | - S Senthivel
- Agricultural Research Station, Tamil Nadu Agricultural University (TNAU), Paramakudi, 623707 India
| | - R Chandra Babu
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| |
Collapse
|
38
|
Bushakra JM, Lewers KS, Staton ME, Zhebentyayeva T, Saski CA. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). BMC Plant Biol 2015; 15:258. [PMID: 26499487 PMCID: PMC4620654 DOI: 10.1186/s12870-015-0629-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/28/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. METHODS Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs. Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. RESULTS To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. CONCLUSION This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.
Collapse
Affiliation(s)
- Jill M Bushakra
- USDA-ARS, National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR, 97333-2521, USA.
| | - Kim S Lewers
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705-2350, USA.
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 EJ Chapman Drive, 370 PBB, Knoxville, TN, 37996, USA.
| | - Tetyana Zhebentyayeva
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
| | - Christopher A Saski
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
| |
Collapse
|
39
|
Valkonen JP. Elucidation of virus-host interactions to enhance resistance breeding for control of virus diseases in potato. Breed Sci 2015; 65:69-76. [PMID: 25931981 PMCID: PMC4374565 DOI: 10.1270/jsbbs.65.69] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/25/2015] [Indexed: 05/03/2023]
Abstract
Potato virus Y (PVY) and Potato mop-top virus (PMTV) are viruses whose geographical distribution is expanding and economic losses are increasing, in contrast to most of other viruses infecting potato crops. Most potato cultivars lack broad-spectrum resistance to the new, genetically complex strains of PVY, and no efficient resistance to PMTV is known in potato. Control of the vectors of these viruses is not an efficient or possible strategy to prevent infections. Studies on molecular virus-host interactions can discover plant genes that are important to viral infection or antiviral defence. Both types of genes may be utilized in resistance breeding, which is discussed in this paper. The advanced gene technologies provide means to fortify potato cultivars with effective virus resistance genes or mutated, non-functional host factors that interfere with virus infection.
Collapse
Affiliation(s)
- Jari P.T. Valkonen
- Department of Agricultural Sciences,
P O Box 27, FI-00014 University of Helsinki,
Finland
| |
Collapse
|
40
|
Venkatesh TV, Cook K, Liu B, Perez T, Willse A, Tichich R, Feng P, Harrigan GG. Compositional differences between near-isogenic GM and conventional maize hybrids are associated with backcrossing practices in conventional breeding. Plant Biotechnol J 2015; 13:200-10. [PMID: 25196222 DOI: 10.1111/pbi.12248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/14/2014] [Accepted: 07/29/2014] [Indexed: 05/03/2023]
Abstract
Here, we show that differences between genetically modified (GM) and non-GM comparators cannot be attributed unequivocally to the GM trait, but arise because of minor genomic differences in near-isogenic lines. Specifically, this study contrasted the effect of three GM traits (drought tolerance, MON 87460; herbicide resistance, NK603; insect protection, MON 89034) on maize grain composition relative to the effects of residual genetic variation from backcrossing. Important features of the study included (i) marker-assisted backcrossing to generate genetically similar inbred variants for each GM line, (ii) high-resolution genotyping to evaluate the genetic similarity of GM lines to the corresponding recurrent parents and (iii) introgression of the different GM traits separately into a wide range of genetically distinct conventional inbred lines. The F1 hybrids of all lines were grown concurrently at three replicated field sites in the United States during the 2012 growing season, and harvested grain was subjected to compositional analysis. Proximates (protein, starch and oil), amino acids, fatty acids, tocopherols and minerals were measured. The number of statistically significant differences (α = 0.05), as well as magnitudes of difference, in mean levels of these components between corresponding GM variants was essentially identical to that between GM and non-GM controls. The largest sources of compositional variation were the genetic background of the different conventional inbred lines (males and females) used to generate the maize hybrids and location. The lack of any compositional effect attributable to GM suggests the development of modern agricultural biotechnology has been accompanied by a lack of any safety or nutritional concerns.
Collapse
|
41
|
Larkan NJ, Lydiate DJ, Yu F, Rimmer SR, Borhan MH. Co-localisation of the blackleg resistance genes Rlm2 and LepR3 on Brassica napus chromosome A10. BMC Plant Biol 2014; 14:387. [PMID: 25551287 PMCID: PMC4302512 DOI: 10.1186/s12870-014-0387-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/15/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The protection of canola (Brassica napus) crops against blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, is largely mediated by race-specific resistance genes (R-genes). While many R-genes effective against blackleg disease have been identified in Brassica species, information of the precise genomic locations of the genes is limited. RESULTS In this study, the Rlm2 gene for resistance to blackleg, located on chromosome A10 of the B. napus cultivar 'Glacier', was targeted for fine mapping. Molecular markers tightly linked to the gene were developed for use in mapping the resistance locus and defining the physical interval in B. napus. Rlm2 was localised to a 5.8 cM interval corresponding to approximately 873 kb of the B. napus chromosome A10. CONCLUSION The recently-cloned B. napus R-gene, LepR3, occupies the same region of A10 as Rlm2 and analysis of the putative B. napus and B. rapa genes in the homologous region identified several additional candidate defense-related genes that may control Rlm2 function.
Collapse
Affiliation(s)
- Nicholas J Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 SK Canada
| | - Derek J Lydiate
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 SK Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 SK Canada
| | - S Roger Rimmer
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 SK Canada
| | - M Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 SK Canada
| |
Collapse
|
42
|
Kumar A, Dixit S, Ram T, Yadaw RB, Mishra KK, Mandal NP. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches. J Exp Bot 2014; 65:6265-78. [PMID: 25205576 PMCID: PMC4223988 DOI: 10.1093/jxb/eru363] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1 , qDTY 2.2 , qDTY 3.1 , qDTY 3.2 , qDTY 6.1 , and qDTY 12.1 ) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding.
Collapse
Affiliation(s)
- Arvind Kumar
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - T Ram
- Directorate of Rice Research (DRR), Rajendra Nagar, Hyderabad, India
| | - R B Yadaw
- National Rice Research Project (NRRP), Hardinath, Nepal
| | - K K Mishra
- National Rice Research Project (NRRP), Hardinath, Nepal
| | - N P Mandal
- Central Rainfed Rice Research Station (CRURRS), Hazaribagh, Jharkhand, India
| |
Collapse
|
43
|
Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A 2013; 110:20431-6. [PMID: 24297875 PMCID: PMC3870739 DOI: 10.1073/pnas.1310790110] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.
Collapse
Affiliation(s)
- Daisuke Fujita
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- National Agriculture and Food Research Organization, Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan; and
| | - Kurniawan Rudi Trijatmiko
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
| | - Analiza Grubanzo Tagle
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
| | - Maria Veronica Sapasap
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
| | - Yohei Koide
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuhiro Sasaki
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Nikolaos Tsakirpaloglou
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
| | - Ritchel Bueno Gannaban
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
| | - Takeshi Nishimura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Seiji Yanagihara
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Yoshimichi Fukuta
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Tomokazu Koshiba
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Inez Hortense Slamet-Loedin
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
| | - Tsutomu Ishimaru
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Nobuya Kobayashi
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- National Agriculture and Food Research Organization, Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan; and
| |
Collapse
|
44
|
Suh JP, Jeung JU, Noh TH, Cho YC, Park SH, Park HS, Shin MS, Kim CK, Jena KK. Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice. Rice (N Y) 2013; 6:5. [PMID: 24280417 PMCID: PMC4883717 DOI: 10.1186/1939-8433-6-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality. RESULTS Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL. CONCLUSIONS The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will have a high impact on the yield stability and sustainability of rice productivity.
Collapse
Affiliation(s)
- Jung-Pil Suh
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Ji-Ung Jeung
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Tae-Hwan Noh
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Young-Chan Cho
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - So-Hyun Park
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Hyun-Su Park
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Mun-Sik Shin
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Chung-Kon Kim
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Kshirod K Jena
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO, Box 7777, Metro Manila, Philippines
| |
Collapse
|
45
|
Welsh CE, McMillan L. Accelerating the inbreeding of multi-parental recombinant inbred lines generated by sibling matings. G3 (Bethesda) 2012; 2:191-8. [PMID: 22384397 DOI: 10.1534/g3.111.001784] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/06/2011] [Indexed: 11/26/2022]
Abstract
Inbred model organisms are powerful tools for genetic studies because they provide reproducible genomes for use in mapping and genetic manipulation. Generating inbred lines via sibling matings, however, is a costly undertaking that requires many successive generations of breeding, during which time many lines fail. We evaluated several approaches for accelerating inbreeding, including the systematic use of back-crosses and marker-assisted breeder selection, which we contrasted with randomized sib-matings. Using simulations, we explored several alternative breeder-selection methods and monitored the gain and loss of genetic diversity, measured by the number of recombination-induced founder intervals, as a function of generation. For each approach we simulated 100,000 independent lines to estimate distributions of generations to achieve full-fixation as well as to achieve a mean heterozygosity level equal to 20 generations of randomized sib-mating. Our analyses suggest that the number of generations to fully inbred status can be substantially reduced with minimal impact on genetic diversity through combinations of parental backcrossing and marker-assisted inbreeding. Although simulations do not consider all confounding factors underlying the inbreeding process, such as a loss of fecundity, our models suggest many viable alternatives for accelerating the inbreeding process.
Collapse
|
46
|
Cary JW, Rajasekaran K, Brown RL, Luo M, Chen ZY, Bhatnagar D. Developing resistance to aflatoxin in maize and cottonseed. Toxins (Basel) 2011; 3:678-96. [PMID: 22069734 PMCID: PMC3202838 DOI: 10.3390/toxins3060678] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 06/14/2011] [Accepted: 06/16/2011] [Indexed: 11/26/2022] Open
Abstract
At this time, no "magic bullet" for solving the aflatoxin contamination problem in maize and cottonseed has been identified, so several strategies must be utilized simultaneously to ensure a healthy crop, free of aflatoxins. The most widely explored strategy for the control of aflatoxin contamination is the development of preharvest host resistance. This is because A. flavus infects and produces aflatoxins in susceptible crops prior to harvest. In maize production, the host resistance strategy has gained prominence because of advances in the identification of natural resistance traits. However, native resistance in maize to aflatoxin contamination is polygenic and complex and, therefore, markers need to be identified to facilitate the transfer of resistance traits into agronomically viable genetic backgrounds while limiting the transfer of undesirable traits. Unlike maize, there are no known cotton varieties that demonstrate enhanced resistance to A. flavus infection and aflatoxin contamination. For this reason, transgenic approaches are being undertaken in cotton that utilize genes encoding antifungal/anti-aflatoxin factors from maize and other sources to counter fungal infection and toxin production. This review will present information on preharvest control strategies that utilize both breeding and native resistance identification approaches in maize as well as transgenic approaches in cotton.
Collapse
Affiliation(s)
- Jeffrey W. Cary
- United States Department of Agriculture-Agriculture Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA; (K.R.); (R.L.B.); (M.L.); (D.B.)
| | - Kanniah Rajasekaran
- United States Department of Agriculture-Agriculture Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA; (K.R.); (R.L.B.); (M.L.); (D.B.)
| | - Robert L. Brown
- United States Department of Agriculture-Agriculture Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA; (K.R.); (R.L.B.); (M.L.); (D.B.)
| | - Meng Luo
- United States Department of Agriculture-Agriculture Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA; (K.R.); (R.L.B.); (M.L.); (D.B.)
| | - Zhi-Yuan Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA;
| | - Deepak Bhatnagar
- United States Department of Agriculture-Agriculture Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA; (K.R.); (R.L.B.); (M.L.); (D.B.)
| |
Collapse
|
47
|
Lieberei R. South American leaf blight of the rubber tree (Hevea spp.): new steps in plant domestication using physiological features and molecular markers. Ann Bot 2007; 100:1125-42. [PMID: 17650512 PMCID: PMC2759241 DOI: 10.1093/aob/mcm133] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rubber trees (Hevea spp.) are perennial crops of Amazonian origin that have been spread over the whole tropical belt to guarantee worldwide production of natural rubber. This crop plant has found its place in many national economies of producing countries, and although its domestication by selection of suitable genotypes was very slow, it contributes a lot to the welfare of small farmers worldwide. Its development is limited by severe diseases. In South America, the main fungal disease of rubber trees is the South American leaf blight (SALB) caused by the ascomycete Microcyclus ulei. This fungus inhibits natural rubber production on a commercial scale in South and Central America. SCOPE The disease is still restricted to its continent of origin, but its potential to be distributed around the world rises with every transcontinental airline connection that directly links tropical regions. The need to develop control measures against the disease is an urgent task and must be carried out on an international scale. All control efforts so far taken since 1910 have ended in a miserable failure. Even the use of modern systemic fungicides and use of greatly improved application techniques have failed to prevent large losses and dieback of trees. The results of research dealing with both the disease and the pathosystem over more than 50 years are summarized and placed into perspective. FUTURE PROSPECTS A detailed knowledge of this host-pathogen combination requires understanding of the dynamics of Hevea leaf development, the biochemical potential for cyanide liberation, and molecular data for several types of resistance factors. Resolution of the Hevea-SALB problem may serve as a model for future host-pathogen studies of perennial plants requiring a holistic approach.
Collapse
Affiliation(s)
- Reinhard Lieberei
- Biocenter Klein Flottbek and Botanical Garden, University of Hamburg, Unit of Applied Ecology and Crop Science, Ohnhorststr. 16, D-22609 Hamburg, Germany.
| |
Collapse
|