1
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Tan Q, Zhou C, Xu P, Huang X, Pan Z, Wei Y, Wang W, Wang L. Effects of Substrate Composition on the Growth Traits of Grafted Seedling in Macadamia ( Macadamia integrifolia) Nuts. PLANTS (BASEL, SWITZERLAND) 2024; 13:1700. [PMID: 38931133 PMCID: PMC11207545 DOI: 10.3390/plants13121700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Macadamia nut plantings in China are expanding year by year. In order to breed and promote superior varieties, this study analyzed the effects of different rootstocks and scions on the survival rate of grafted seedlings, and then selected the best substrate composition for plant growth. The results showed that the survival rate of the HAES788 variety as rootstock and Guire No. 1 as scion was the highest, reaching 96%. The optimal grafting time in December was better than that in March. Furthermore, among 16 substrate formulations, T12, T13, T15, and T16 had advantages of agglomerated soil and more well-developed root systems compared to the CK made of loess. The plant height, stem diameter, leaf length, leaf width, and dry weight of the aboveground and underground parts of the grafted seedlings planted in these substrate formulations were significantly higher than those plants planted in the CK. In addition, the substrate formulations T12, T13, T15, and T16 significantly improved the organic matter, total nitrogen, and total potassium content of the substrate soils, but little improvement was observed for total phosphorus content after 13 months. Overall, macadamia grafting times are best in December, with HAES788 and Guire No. 1 being the best rootstock and scion. The optimal substrate formulations are T12, T13, T15, and T16. This study provides a solid foundation for the production of high-quality macadamia plants.
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Affiliation(s)
- Qiujin Tan
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Chunheng Zhou
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Peng Xu
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Xiyun Huang
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Zhenzhen Pan
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Yuanrong Wei
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Wenlin Wang
- Guangxi South Subtropical Agricultural Research Institute, Longzhou 532415, China (X.H.)
| | - Lifeng Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Guangxi Academy of Agricultural Sciences, Nanning 530007, China
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2
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Yang J, Ning C, Liu Z, Zheng C, Mao Y, Wu Q, Wang D, Liu M, Zhou S, Yang L, He L, Liu Y, He C, Chen J, Liu J. Genome-Wide Characterization of PEBP Gene Family and Functional Analysis of TERMINAL FLOWER 1 Homologs in Macadamia integrifolia. PLANTS (BASEL, SWITZERLAND) 2023; 12:2692. [PMID: 37514306 PMCID: PMC10385423 DOI: 10.3390/plants12142692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Edible Macadamia is one of the most important commercial nut trees cultivated in many countries, but its large tree size and long juvenile period pose barriers to commercial cultivation. The short domestication period and well-annotated genome of Macadamia integrifolia create great opportunities to breed commercial varieties with superior traits. Recent studies have shown that members of the phosphatidylethanolamine binding protein (PEBP) family play pivotal roles in regulating plant architecture and flowering time in various plants. In this study, thirteen members of MiPEBP were identified in the genome of M. integrifolia, and they are highly similarity in both motif and gene structure. A phylogenetic analysis divided the MiPEBP genes into three subfamilies: MFT-like, FT-like and TFL1-like. We subsequently identified two TERMINAL FLOWER 1 homologues from the TFL1-like subfamily, MiTFL1 and MiTFL1-like, both of which were highly expressed in stems and vegetative shoots, while MiTFL1-like was highly expressed in young leaves and early flowers. A subcellular location analysis revealed that both MiTFL1 and MiTFL1-like are localized in the cytoplasm and nucleus. The ectopic expression of MiTFL1 can rescue the early-flowering and terminal-flower phenotypes in the tfl1-14 mutant of Arabidopsis thaliana, and it indicates the conserved functions in controlling the inflorescence architecture and flowering time. This study will provide insight into the isolation of PEBP family members and the key targets for breeding M. integrifolia with improved traits in plant architecture and flowering time.
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Affiliation(s)
- Jing Yang
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Conghui Ning
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Ziyan Liu
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Mingli Liu
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Liling Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Chengzhong He
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
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3
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Maniruzzaman S, Rahman MA, Hasan M, Rasul MG, Molla AH, Khatun H, Iftekharuddaula KM, Kabir MS, Akter S. Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice. Int J Mol Sci 2023; 24:11141. [PMID: 37446320 DOI: 10.3390/ijms241311141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT, and salT locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.
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Affiliation(s)
- Sheikh Maniruzzaman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Akhlasur Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Mehfuz Hasan
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mohammad Golam Rasul
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Abul Hossain Molla
- Department of Environmental Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Hasina Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - K M Iftekharuddaula
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Md Shahjahan Kabir
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Salma Akter
- Plant Physiology Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
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4
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Wilkinson MJ, Yamashita R, James ME, Bally ISE, Dillon NL, Ali A, Hardner CM, Ortiz-Barrientos D. The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool. Sci Rep 2022; 12:20614. [PMID: 36450793 PMCID: PMC9712640 DOI: 10.1038/s41598-022-24800-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/21/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.
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Affiliation(s)
- Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Risa Yamashita
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maddie E James
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian S E Bally
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Natalie L Dillon
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Asjad Ali
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia
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5
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Wang P, Mo Y, Wang Y, Fei Y, Huang J, Ni J, Xu ZF. Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia. FRONTIERS IN PLANT SCIENCE 2022; 13:1007266. [PMID: 36388568 PMCID: PMC9646992 DOI: 10.3389/fpls.2022.1007266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
As an important nut crop species, macadamia continues to gain increased amounts of attention worldwide. Nevertheless, with the vast increase in macadamia omic data, it is becoming difficult for researchers to effectively process and utilize the information. In this work, we developed the first integrated germplasm and genomic database for macadamia (MacadamiaGGD), which includes five genomes of four species; three chloroplast and mitochondrial genomes; genome annotations; transcriptomic data for three macadamia varieties, germplasm data for four species and 262 main varieties; nine genetic linkage maps; and 35 single-nucleotide polymorphisms (SNPs). The database serves as a valuable collection of simple sequence repeat (SSR) markers, including both markers that are based on macadamia genomic sequences and developed in this study and markers developed previously. MacadamiaGGD is also integrated with multiple bioinformatic tools, such as search, JBrowse, BLAST, primer designer, sequence fetch, enrichment analysis, multiple sequence alignment, genome alignment, and gene homology annotation, which allows users to conveniently analyze their data of interest. MacadamiaGGD is freely available online (http://MacadamiaGGD.net). We believe that the database and additional information of the SSR markers can help scientists better understand the genomic sequence information of macadamia and further facilitate molecular breeding efforts of this species.
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Affiliation(s)
- Pan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yi Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yuchong Fei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Jianting Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Jun Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
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6
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The Effects of Pollen Source on the Fatty Acid profile of Macadamia Kernels. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice. PLANTS 2022; 11:plants11111409. [PMID: 35684182 PMCID: PMC9183132 DOI: 10.3390/plants11111409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022]
Abstract
Rice is the world’s most important food crop, providing the daily calorie intake for more than half of the world’s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly reduce rice productivity. Salinity, one of the major abiotic stresses, reduces rice yield worldwide. This study was conducted to determine new quantitative trait loci (QTLs) that regulate salt tolerance in rice seedlings. One F2:3 mapping population was derived from a cross between BRRI dhan49 (a popular but sensitive rainfed rice variety) and Akundi (a salt-tolerant rice landrace in Bangladesh used as a donor parent). The 1k-Rice Custom Amplicon (1k-RiCA) single-nucleotide polymorphism (SNP) markers were used to genotype this mapping population. After removing segregation distortion and monomorphic markers, 884 SNPs generated a 1526.8 cM-long genetic linkage map with a mean marker density of 1.7 cM for the 12 linkage groups. By exploiting QGene and ICIM-ADD, a sum of 15 QTLs for nine traits was identified in salt stress on seven chromosomes. Four important genomic loci were identified (qSES1, qSL1, qSUR1 and qRL1) on chromosome 1. Out of these 15 QTLs, 14 QTLs are unique, as no other study has mapped in the same chromosomal location. We also detected 15 putative candidate genes and their functions. The ICIM-EPI approach identified 43 significant pairwise epistasis interactions between regions associated with and unassociated with QTLs. Apart from more well-known donors, Akundi serves as an important new donor source for global salt tolerance breeding initiatives, including Bangladesh. The introgression of the novel QTLs identified in this study will accelerate the development of new salt-tolerant varieties that are highly resistant to salt stress using marker-enabled breeding.
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8
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Zakeel MCM, Alam M, Geering ADW, Topp B, Akinsanmi OA. Discovery of Single Nucleotide Polymorphisms for Resistance to Abnormal Vertical Growth in Macadamia. FRONTIERS IN PLANT SCIENCE 2021; 12:756815. [PMID: 35003155 PMCID: PMC8739493 DOI: 10.3389/fpls.2021.756815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked sample analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance.
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Affiliation(s)
- Mohamed Cassim Mohamed Zakeel
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Mobashwer Alam
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Nambour, QLD, Australia
| | - Andrew D. W. Geering
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Bruce Topp
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Nambour, QLD, Australia
| | - Olufemi A. Akinsanmi
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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9
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McCartney AM, Hilario E, Choi S, Guhlin J, Prebble JM, Houliston G, Buckley TR, Chagné D. An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome. Mol Ecol Resour 2021; 21:2125-2144. [PMID: 33955186 PMCID: PMC8362059 DOI: 10.1111/1755-0998.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022]
Abstract
We used long read sequencing data generated from Knightia excelsa, a nectar-producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Subsampling highlighted that input data with longer read lengths but perhaps lower coverage constructed more contiguous, kmers and gene-complete assemblies than short read length input data with higher coverage. The final genome assembly was constructed into 14 pseudochromosomes using an initial flye long read assembly, a racon/medaka/pilon combined polishing strategy, salsa2 and allhic scaffolding, juicebox curation, and Macadamia linkage map validation. We highlighted the importance of developing assembly workflows based on the volume and read length of sequencing data and established a robust set of quality metrics for generating high-quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by Hi-C data and that assembly scaffolding was more successful when the underlying contig assembly was of higher accuracy. These findings provide insight into how quality assessment tools can be implemented throughout genome assembly pipelines to inform the de novo reconstruction of a high-quality genome assembly for nonmodel organisms.
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Affiliation(s)
- Ann M. McCartney
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
| | - Elena Hilario
- Genomics AotearoaDunedinNew Zealand
- The New Zealand Institute for Plant and Food Research (Plant & Food Research)SandringhamNew Zealand
| | - Seung‐Sub Choi
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Joseph Guhlin
- Genomics AotearoaDunedinNew Zealand
- University of OtagoDunedinNew Zealand
| | - Jessica M. Prebble
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Gary Houliston
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Thomas R. Buckley
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - David Chagné
- Genomics AotearoaDunedinNew Zealand
- Plant & Food ResearchFitzherbert, Palmerston NorthNew Zealand
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10
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O'Connor KM, Hayes BJ, Hardner CM, Alam M, Henry RJ, Topp BL. Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population. BMC Genomics 2021; 22:370. [PMID: 34016055 PMCID: PMC8139092 DOI: 10.1186/s12864-021-07694-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Background Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations. Results Narrow-sense heritability of yield and yield stability was low (h2=0.30 and 0.04, respectively). Prediction accuracy for yield was 0.57 for predictions across related populations and 0.14 when predicted across unrelated populations. Accuracy of prediction of yield stability was high (r=0.79) for predictions across related populations. Predicted genetic gain of yield using GS in related populations was 474g/year, more than double that of traditional breeding methods (226g/year), due to the halving of generation length from 8 to 4years. Conclusions The results of this study indicate that the incorporation of GS for yield into the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07694-z.
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Affiliation(s)
- Katie M O'Connor
- Queensland Department of Agriculture and Fisheries, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia.
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Bruce L Topp
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia
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Ganie SA, Wani SH, Henry R, Hensel G. Improving rice salt tolerance by precision breeding in a new era. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101996. [PMID: 33444976 DOI: 10.1016/j.pbi.2020.101996] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 05/03/2023]
Abstract
Rice is a premier staple food that constitutes the bulk of the daily diet of the majority of people in Asia. Agricultural productivity must be boosted to support this huge demand for rice. However, production is jeopardized by soil salinity. Advances in whole-genome sequencing, marker-assisted breeding strategies, and targeted mutagenesis have substantially improved the toolbox of today's breeders. Given that salinity has a major influence on rice at both the seedling and reproductive stages, understanding and manipulating this trait will have an enormous impact on sustainable production. This article summarizes recent developments in the understanding of the mechanisms of salt tolerance and how state-of-the-art tools such as RNA guided CRISPR endonuclease technology including targeted mutagenesis or base and prime editing can help in gene discovery and functional analysis as well as in transferring favorable alleles into elite breeding material to speed the breeding of salt-tolerant rice cultivars.
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Affiliation(s)
- Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan 731235, West Bengal, India.
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani - 192101, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, J&K, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, OT Gatersleben, 06466 Seeland, Germany; Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic.
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12
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Chromosome-Scale Assembly and Annotation of the Macadamia Genome ( Macadamia integrifolia HAES 741). G3-GENES GENOMES GENETICS 2020; 10:3497-3504. [PMID: 32747341 PMCID: PMC7534425 DOI: 10.1534/g3.120.401326] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.
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Wang W, Xu J, Fang H, Li Z, Li M. Advances and challenges in medicinal plant breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110573. [PMID: 32771174 DOI: 10.1016/j.plantsci.2020.110573] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/08/2020] [Accepted: 06/19/2020] [Indexed: 05/04/2023]
Abstract
Large-scale cultivation of medicinal plants is the most rapid and effective means of addressing the disparity between the supply and demand of medicinal plants. To achieve this scale of production, breeding studies are necessary for further development of medicinal plant cultivation. Although advances have been made in the breeding of some medicinal plants, a number of challenges remain, owing to the particularity and complexity in determining the breeding target. Additionally, there are limitations associated with research on traditional and modern breeding methods for medicinal plants. In this review, we summarize and analyze the selection strategies for breeding direction and breeding models, and emphasize the importance of breeding research in promoting the breeding of medicinal plants.
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Affiliation(s)
- Wenle Wang
- Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot, Inner Mongolia, China
| | - Jinfan Xu
- Baotou Medical College, Baotou, Inner Mongolia, China
| | - Huiyong Fang
- School of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, Hebei, China
| | - Zhijun Li
- Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia, China
| | - Minhui Li
- Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot, Inner Mongolia, China; Baotou Medical College, Baotou, Inner Mongolia, China.
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