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Hawliczek A, Borzęcka E, Tofil K, Alachiotis N, Bolibok L, Gawroński P, Siekmann D, Hackauf B, Dušinský R, Švec M, Bolibok-Brągoszewska H. Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement. BMC PLANT BIOLOGY 2023; 23:323. [PMID: 37328739 PMCID: PMC10273710 DOI: 10.1186/s12870-023-04337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. RESULTS Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. CONCLUSIONS Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.
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Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, Enschede, The Netherlands
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | | | | | - Roman Dušinský
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Miroslav Švec
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland.
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Kumari A, Sharma D, Sharma P, Wang C, Verma V, Patil A, Imran M, Singh MP, Kumar K, Paritosh K, Caragea D, Kapoor S, Chandel G, Grover A, Jagadish SVK, Katiyar-Agarwal S, Agarwal M. Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1133115. [PMID: 36968399 PMCID: PMC10031497 DOI: 10.3389/fpls.2023.1133115] [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: 12/28/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Divya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Vibha Verma
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arun Patil
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Md Imran
- Department of Botany, University of Delhi, Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kuldeep Kumar
- National Institute for Plant Biotechnology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, New Delhi, India
| | - Doina Caragea
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Girish Chandel
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | | | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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Dai M, Yang X, Chen Q, Bai Z. Comprehensive genomic identification of cotton starch synthase genes reveals that GhSS9 regulates drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1163041. [PMID: 37089638 PMCID: PMC10113511 DOI: 10.3389/fpls.2023.1163041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Introduction Starch metabolism is involved in the stress response. Starch synthase (SS) is the key enzyme in plant starch synthesis, which plays an indispensable role in the conversion of pyrophosphoric acid to starch. However, the SS gene family in cotton has not been comprehensively identified and systematically analyzed. Result In our study, a total of 76 SS genes were identified from four cotton genomes and divided into five subfamilies through phylogenetic analysis. Genetic structure analysis proved that SS genes from the same subfamily had similar genetic structure and conserved sequences. A cis-element analysis of the SS gene promoter showed that it mainly contains light response elements, plant hormone response elements, and abiotic stress elements, which indicated that the SS gene played key roles not only in starch synthesis but also in abiotic stress response. Furthermore, we also conducted a gene interaction network for SS proteins. Silencing GhSS9 expression decreased the resistance of cotton to drought stress. These findings suggested that SS genes could be related to drought stress in cotton, which provided theoretical support for further research on the regulation mechanism of SS genes on abiotic starch synthesis and sugar levels.
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Affiliation(s)
- Maohua Dai
- Dryland Farming Institute, Hebei Academy of Agricultural and Forestry Sciences/Hebei Key Laboratory of Crops Drought Resistance, Hengshui, China
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Xiaomin Yang
- Dryland Farming Institute, Hebei Academy of Agricultural and Forestry Sciences/Hebei Key Laboratory of Crops Drought Resistance, Hengshui, China
- Cash Crop Research Institute of Jiangxi Province, Jiujiang, Jiangxi, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- *Correspondence: Quanjia Chen, ; Zhigang Bai,
| | - Zhigang Bai
- Cash Crop Research Institute of Jiangxi Province, Jiujiang, Jiangxi, China
- *Correspondence: Quanjia Chen, ; Zhigang Bai,
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Panja S, Kar RK, Chandra Dey P, Dey N. Underpinning the soft nature of soak-n-eat rice - A physicochemical and molecular approach. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Maung TZ, Chu SH, Park YJ. Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II ( GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). Foods 2021; 10:2359. [PMID: 34681408 PMCID: PMC8535093 DOI: 10.3390/foods10102359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
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6
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Jo J, Kim Y, Kim GW, Kwon JK, Kang BC. Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum. FRONTIERS IN PLANT SCIENCE 2021; 12:769473. [PMID: 34764974 PMCID: PMC8576353 DOI: 10.3389/fpls.2021.769473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/07/2021] [Indexed: 05/05/2023]
Abstract
Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed by GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying the various filter options to obtain a comparable dataset of SNPs. Here, we developed a panel of a multiplex targeted sequencing method, genotyping-in-thousands by sequencing (GT-seq), to genotype SNPs in Capsicum spp. Previously developed Fluidigm® SNP markers were converted to GT-seq markers and combined with new GT-seq markers developed using SNP information obtained through GBS. We then optimized multiplex PCR conditions: we obtained the highest genotyping rate when the first PCR consisted of 25 cycles. In addition, we determined that 101 primer pairs performed best when amplifying target sequences of 79 bp. We minimized interference of multiplex PCR by primer dimer formation using the PrimerPooler program. Using our GT-seq pipeline on Illumina Miseq and Nextseq platforms, we genotyped up to 1,500 (Miseq) and 1,300 (Nextseq) samples for the optimum panel size of 100 loci. To allow the genotyping of Capsicum species, we designed 332 informative GT-seq markers from Fluidigm SNP markers and GBS-derived SNPs. This study illustrates the first application of GT-seq in crop plants. The GT-seq marker set developed here will be a useful tool for molecular breeding of peppers in the future.
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8
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Hawliczek A, Bolibok L, Tofil K, Borzęcka E, Jankowicz-Cieślak J, Gawroński P, Kral A, Till BJ, Bolibok-Brągoszewska H. Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions. BMC Genomics 2020; 21:845. [PMID: 33256606 PMCID: PMC7706248 DOI: 10.1186/s12864-020-07240-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Discovery of DNA variations is an important step in the efficient use of these resources. While technologies have improved and costs dropped, it remains impractical to consider resequencing millions of accessions. Candidate genes are known for most agronomic traits, providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples from an accession need to be evaluated to recover available alleles. To address this we developed a pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale L.). RESULTS Using the amplicon sequencing approach 95 rye accessions of different improvement status and worldwide origin, each represented by a pooled sample comprising DNA of 96 individual plants, were evaluated for sequence variation in six candidate genes with significant functions on biotic and abiotic stress resistance, and seed quality. Seventy-four predicted deleterious variants were identified using multiple algorithms. Rare variants were recovered including those found only in a low percentage of seed. CONCLUSIONS We conclude that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation. A large extent of within-population heterogeneity revealed in the study provides an important point for consideration during rye germplasm conservation and utilization efforts.
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Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Joanna Jankowicz-Cieślak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Adam Kral
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria.
- Veterinary Genetics Laboratory, University of California, Davis, Davis, California, USA.
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.
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Re-sequencing Resources to Improve Starch and Grain Quality in Rice. Methods Mol Biol 2018. [PMID: 30397808 DOI: 10.1007/978-1-4939-8914-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.
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Li Q, Liu X, Zhang C, Jiang L, Jiang M, Zhong M, Fan X, Gu M, Liu Q. Rice Soluble Starch Synthase I: Allelic Variation, Expression, Function, and Interaction With Waxy. FRONTIERS IN PLANT SCIENCE 2018; 9:1591. [PMID: 30483281 PMCID: PMC6243471 DOI: 10.3389/fpls.2018.01591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/15/2018] [Indexed: 05/07/2023]
Abstract
Starch, which is composed of amylose and amylopectin, is the key determinant of rice quality. Amylose is regulated by the Waxy (Wx) gene, whereas amylopectin is coordinated by various enzymes including eight soluble starch synthases (SSSs), of which SSSI accounts for ∼70% of the total SSS activity in cereal endosperm. Although great progress has been made in understanding SSSI gene expression and function, allelic variation and its effects on gene expression, rice physicochemical properties and qualities, and interactions with the Wx gene remain unclear. Herein, SSSI nucleotide polymorphisms were analyzed in 165 rice varieties using five distinct molecular markers, three of which reside in an SSSI promoter and might account for a higher expression of the SSSIi allele in indica ssp. than of the SSSIj allele in japonica ssp. The results of SSSI promoter-Beta-Glucuronidase (β-GUS) analysis were consistent with the expression results. Moreover, analysis of near isogenic lines (NILs) in the Nipponbare (Nip) background showed that Nip (SSSIi ) and Nip (SSSIj ) differed in their thermal properties, gel consistency (GC), and granule crystal structure. Knockdown of SSSI expression using the SSSI-RNA interference (RNAi) construct in both japonica and indica backgrounds caused consistent changes in most tested physicochemical characteristics except GC. Moreover, taste value analysis (TVA) showed that introduction of the SSSI allele in indica or knockdown of SSSI expression in japonica cultivars significantly reduced the comprehensive taste value, which was consistent with the superior taste of japonica against indica. Furthermore, to test the potential interaction between SSSI and different Wx alleles, three NILs within the Wx locus were generated in the indica cv. Longtefu (LTF) background, which were designated as LTF (Wxa ), LTF (Wxb ), and LTF (wx). The SSSI-RNAi construct was also introduced into these three NILs, and physiochemical analysis confirmed that the knockdown of SSSI significantly increased the rice apparent amylose content (AAC) only in the Wxa and Wxb background and caused different changes in GC in the NILs. Therefore, the effect of SSSI variation on rice quality also depends on its crosstalk with other factors, especially the Wx gene. These findings provide fundamental knowledge for future breeding of rice with premium eating and cooking qualities.
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Affiliation(s)
- Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xinyan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Li Jiang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Meiyan Jiang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Min Zhong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Qiaoquan Liu,
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Onda Y, Takahagi K, Shimizu M, Inoue K, Mochida K. Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:201. [PMID: 29628929 PMCID: PMC5876661 DOI: 10.3389/fpls.2018.00201] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/02/2018] [Indexed: 05/20/2023]
Abstract
Next-generation sequencing (NGS) technologies have enabled genome re-sequencing for exploring genome-wide polymorphisms among individuals, as well as targeted re-sequencing for the rapid and simultaneous detection of polymorphisms in genes associated with various biological functions. Therefore, a simple and robust method for targeted re-sequencing should facilitate genotyping in a wide range of biological fields. In this study, we developed a simple, custom, targeted re-sequencing method, designated "multiplex PCR targeted amplicon sequencing (MTA-seq)," and applied it to the genotyping of the model grass Brachypodium distachyon. To assess the practical usability of MTA-seq, we applied it to the genotyping of genome-wide single-nucleotide polymorphisms (SNPs) identified in natural accessions (Bd1-1, Bd3-1, Bd21-3, Bd30-1, Koz-1, Koz-3, and Koz-4) by comparing the re-sequencing data with that of reference accession Bd21. Examination of SNP-genotyping accuracy in 443 amplicons from eight parental accessions and an F1 progeny derived by crossing of Bd21 and Bd3-1 revealed that ~95% of the SNPs were correctly called. The assessment suggested that the method provided an efficient framework for accurate and robust SNP genotyping. The method described here enables easy design of custom target SNP-marker panels in various organisms, facilitating a wide range of high-throughput genetic applications, such as genetic mapping, population analysis, molecular breeding, and genomic diagnostics.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kotaro Takahagi
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resource, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida
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12
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Wang DR, Han R, Wolfrum EJ, McCouch SR. The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa. THE NEW PHYTOLOGIST 2017; 215:658-671. [PMID: 28556941 PMCID: PMC5488208 DOI: 10.1111/nph.14614] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/28/2017] [Indexed: 05/13/2023]
Abstract
Harnessing stem carbohydrate dynamics in grasses offers an opportunity to help meet future demands for plant-based food, fiber and fuel production, but requires a greater understanding of the genetic controls that govern the synthesis, interconversion and transport of such energy reserves. We map out a blueprint of the genetic architecture of rice (Oryza sativa) stem nonstructural carbohydrates (NSC) at two critical developmental time-points using a subpopulation-specific genome-wide association approach on two diverse germplasm panels followed by quantitative trait loci (QTL) mapping in a biparental population. Overall, 26 QTL are identified; three are detected in multiple panels and are associated with starch-at-maturity, sucrose-at-maturity and NSC-at-heading. They tag OsHXK6 (rice hexokinase), ISA2 (rice isoamylase) and a tandem array of sugar transporters. This study provides the foundation for more in-depth molecular investigation to validate candidate genes underlying rice stem NSC and informs future comparative studies in other agronomically vital grass species.
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Affiliation(s)
- Diane R. Wang
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853‐1901USA
| | - Rongkui Han
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853‐1901USA
| | - Edward J. Wolfrum
- Integrated Biorefinery Research FacilityNational Renewable Energy LabGoldenCO80401USA
| | - Susan R. McCouch
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853‐1901USA
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13
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Xiang X, Kang C, Xu S, Yang B. Combined effects of Wx and SSIIa haplotypes on rice starch physicochemical properties. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:1229-1234. [PMID: 27312246 DOI: 10.1002/jsfa.7854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Wx and SSIIa are central genes for determining starch physicochemical properties and rice endosperm starch is composed of linear amylose, which is entirely synthesized by granule bound starch synthase I (GBSSI, encoded by Wx) and branched amylopectin. In the present study, different haplotypes of rice were examined to investigate the combined effects of pivotal genes in the metabolic chain of starch, Wx and SSIIa. RESULTS Wx haplotypes differed in terms of apparent amylose content (AAC) and gel consistency (GC). The I-3 [haplotype I (Int1T/Ex10C) of Wx and haplotype 3 (A-G-TT) of SSIIa] and the I-4 combinations of rice had better eating and cooking qualities (ECQs) with lower AAC, lower gelatinization temperature (GT) and softer GC. CONCLUSION The characteristic parameters of Rapid Visco-analyser (RVA) could distinguish differences in AAC and GC but not GT. The I-3 and I-4 haplotype combinations of Wx and SSIIa represent key targets for the production of rice with better ECQs. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Xunchao Xiang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, 59 Qinglong Road, Mianyang, 621010, China
| | - Cuifang Kang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Shunju Xu
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Bowen Yang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
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14
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Raja RB, Agasimani S, Jaiswal S, Thiruvengadam V, Sabariappan R, Chibbar RN, Ram SG. EcoTILLING by sequencing reveals polymorphisms in genes encoding starch synthases that are associated with low glycemic response in rice. BMC PLANT BIOLOGY 2017; 17:13. [PMID: 28088172 PMCID: PMC5423428 DOI: 10.1186/s12870-016-0968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/23/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Glycemic response, a trait that is tedious to be assayed in cereal staples, has been identified as a factor correlated with alarmingly increasing prevalence of Type II diabetes. Reverse genetics based discovery of allelic variants associated with this nutritional trait gains significance as they can provide scope for genetic improvement of this factor which is otherwise difficult to target through routine screening methods. RESULTS Through EcoTILLING by sequencing in 512 rice accessions, we report the discovery of six deleterious variants in the genes with potential to increase Resistant Starch (RS) and reduce Hydrolysis Index (HI) of starch. By deconvolution of the variant harbouring EcoTILLING DNA pools, we discovered accessions with a minimum of one to a maximum of three deleterious allelic variants in the candidate genes. CONCLUSIONS Through biochemical assays, we confirmed the potential role of the discovered alleles alone or in combinations in increasing RS the key factor for reduction in glycemic response.
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Affiliation(s)
- Ramadoss Bharathi Raja
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Somanath Agasimani
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Sarita Jaiswal
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Venkatesan Thiruvengadam
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Robin Sabariappan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Ravindra N Chibbar
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Sundaram Ganesh Ram
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India.
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15
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Nida H, Blum S, Zielinski D, Srivastava DA, Elbaum R, Xin Z, Erlich Y, Fridman E, Shental N. Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:349-359. [PMID: 26959378 DOI: 10.1111/tpj.13161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/10/2016] [Accepted: 03/01/2016] [Indexed: 05/29/2023]
Abstract
Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next-generation sequencing to allow such large-scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large-scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost-effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.
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Affiliation(s)
- Habte Nida
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shula Blum
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dina Zielinski
- New York Genome Center, 101 Avenue of the Americas, New York, NY, USA
| | - Dhruv A Srivastava
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Rivka Elbaum
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, US Department of Agriculture/Agricultural Research Service, Lubbock, TX, USA
| | - Yaniv Erlich
- New York Genome Center, 101 Avenue of the Americas, New York, NY, USA
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
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16
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Rathinasabapathi P, Purushothaman N, Parani M. Genome-wide DNA polymorphisms in Kavuni, a traditional rice cultivar with nutritional and therapeutic properties. Genome 2016; 59:363-6. [PMID: 27093133 DOI: 10.1139/gen-2016-0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.
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Affiliation(s)
- Pasupathi Rathinasabapathi
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India.,Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India
| | - Natarajan Purushothaman
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India.,Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India
| | - Madasamy Parani
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India.,Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India
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17
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Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1070-85. [PMID: 26311018 DOI: 10.1111/pbi.12454] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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18
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Anacleto R, Cuevas RP, Jimenez R, Llorente C, Nissila E, Henry R, Sreenivasulu N. Prospects of breeding high-quality rice using post-genomic tools. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1449-66. [PMID: 25993897 DOI: 10.1007/s00122-015-2537-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/08/2015] [Indexed: 05/15/2023]
Abstract
The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized. Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality.
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Affiliation(s)
- Roslen Anacleto
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines,
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19
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Rathinasabapathi P, Purushothaman N, Ramprasad VL, Parani M. Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index. Sci Rep 2015; 5:11303. [PMID: 26068787 PMCID: PMC4464077 DOI: 10.1038/srep11303] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/18/2015] [Indexed: 12/13/2022] Open
Abstract
Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina’s paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, ‘A’ at position 2,386, and ‘C’ at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors.
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Affiliation(s)
- Pasupathi Rathinasabapathi
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu- 603 203, India
| | - Natarajan Purushothaman
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu- 603 203, India
| | | | - Madasamy Parani
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu- 603 203, India
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20
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Luo J, Jobling SA, Millar A, Morell MK, Li Z. Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population. RICE (NEW YORK, N.Y.) 2015; 8:15. [PMID: 25844120 PMCID: PMC4385112 DOI: 10.1186/s12284-015-0046-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/28/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes. RESULTS The allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules. CONCLUSIONS Rice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.
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Affiliation(s)
- Jixun Luo
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
- />College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia
| | - Stephen A Jobling
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
| | - Anthony Millar
- />College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia
| | - Matthew K Morell
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
- />International Rice Research Institute, Maligaya, Muñoz, Nueva Ecija Philippines
| | - Zhongyi Li
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
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21
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Hayward AC, Tollenaere R, Dalton-Morgan J, Batley J. Molecular marker applications in plants. Methods Mol Biol 2015; 1245:13-27. [PMID: 25373746 DOI: 10.1007/978-1-4939-1966-6_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.
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Affiliation(s)
- Alice C Hayward
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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22
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Luo J, Jobling SA, Millar A, Morell MK, Li Z. Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population. RICE (NEW YORK, N.Y.) 2015; 8:15. [PMID: 25844120 DOI: 10.1186./s12284-015-0046-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/28/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes. RESULTS The allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules. CONCLUSIONS Rice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.
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Affiliation(s)
- Jixun Luo
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia ; College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia
| | - Stephen A Jobling
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
| | - Anthony Millar
- College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia
| | - Matthew K Morell
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia ; International Rice Research Institute, Maligaya, Muñoz, Nueva Ecija Philippines
| | - Zhongyi Li
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
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Abstract
The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.
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Liu JJ, Sniezko RA, Sturrock RN, Chen H. Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications. BMC PLANT BIOLOGY 2014; 14:380. [PMID: 25547170 PMCID: PMC4302426 DOI: 10.1186/s12870-014-0380-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/11/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Western white pine (WWP, Pinus monticola Douglas ex D. Don) is of high interest in forest breeding and conservation because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused by the fungus Cronartium ribicola J. C. Fisch). However, WWP lacks genomic resource development and is evolutionarily far away from plants with available draft genome sequences. Here we report a single nucleotide polymorphism (SNP) study by bulked segregation-based RNA-Seq analysis. RESULTS A collection of resistance germplasm was used for construction of cDNA libraries and SNP genotyping. Approximately 36-89 million 2 × 100-bp reads were obtained per library and de-novo assembly generated the first shoot-tip reference transcriptome containing a total of 54,661 unique transcripts. Bioinformatic SNP detection identified >100,000 high quality SNPs in three expressed candidate gene groups: Pinus highly conserved genes (HCGs), differential expressed genes (DEGs) in plant defense response, and resistance gene analogs (RGAs). To estimate efficiency of in-silico SNP discovery, genotyping assay was developed by using Sequenom iPlex and it unveiled SNP success rates from 40.1% to 61.1%. SNP clustering analyses consistently revealed distinct populations, each composed of multiple full-sib seed families by parentage assignment in the WWP germplasm collection. Linkage disequilibrium (LD) analysis identified six genes in significant association with major gene (Cr2) resistance, including three RGAs (two NBS-LRR genes and one receptor-like protein kinase -RLK gene), two HCGs, and one DEG. At least one SNP locus provided an excellent marker for Cr2 selection across P. monticola populations. CONCLUSIONS The WWP shoot tip transcriptome and those validated SNP markers provide novel genomic resources for genetic, evolutionary and ecological studies. SNP loci of those candidate genes associated with resistant phenotypes can be used as positional and functional variation sites for further characterization of WWP major gene resistance against C. ribicola. Our results demonstrate that integration of RNA-seq-based transcriptome analysis and high-throughput genotyping is an effective approach for discovery of a large number of nucleotide variations and for identification of functional gene variants associated with adaptive traits in a non-model species.
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Affiliation(s)
- Jun-Jun Liu
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Richard A Sniezko
- />USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR 97424 USA
| | - Rona N Sturrock
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Hao Chen
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
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Mo YJ, Jeung JU, Shin WC, Kim KY, Ye C, Redoña ED, Kim BK. Effects of allelic variations in starch synthesis-related genes on grain quality traits of Korean nonglutinous rice varieties under different temperature conditions. BREEDING SCIENCE 2014; 64:164-75. [PMID: 24987303 PMCID: PMC4065324 DOI: 10.1270/jsbbs.64.164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/12/2014] [Indexed: 05/07/2023]
Abstract
Influences of allelic variations in starch synthesis-related genes (SSRGs) on rice grain quality were examined. A total of 187 nonglutinous Korean rice varieties, consisting of 170 Japonica and 17 Tongil-type varieties, were grown in the field and in two greenhouse conditions. The percentages of head rice and chalky grains, amylose content, alkali digestion value, and rapid visco-analysis characteristics were evaluated in the three different environments. Among the 10 previously reported SSRG markers used in this study, seven were polymorphic, and four of those showed subspecies-specific allele distributions. Six out of the seven polymorphic SSRG markers were significantly associated with at least one grain quality trait (R (2) > 0.1) across the three different environments. However, the association level and significance were markedly lower when the analysis was repeated using only the 170 Japonica varieties. Similarly, the significant associations between SSRG allelic variations and changes in grain quality traits under increased temperature were largely attributable to the biased allele frequency between the two subpopulations. Our results suggest that within Korean Japonica varieties, these 10 major SSRG loci have been highly fixed during breeding history and variations in grain quality traits might be influenced by other genetic factors.
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Affiliation(s)
- Young-Jun Mo
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Woon-Chul Shin
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Ki-Young Kim
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Changrong Ye
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Edilberto D. Redoña
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Bo-Kyeong Kim
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
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Affiliation(s)
- R. J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
- E-mail: Tel: +61 7 33460551; Fax: +61 7 33460555
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Wambugu PW, Furtado A, Waters DLE, Nyamongo DO, Henry RJ. Conservation and utilization of African Oryza genetic resources. RICE (NEW YORK, N.Y.) 2013; 6:29. [PMID: 24280189 PMCID: PMC4883696 DOI: 10.1186/1939-8433-6-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 05/20/2023]
Abstract
Africa contains a huge diversity of both cultivated and wild rice species. The region has eight species representing six of the ten known genome types. Genetic resources of these species are conserved in various global germplasm repositories but they remain under collected and hence underrepresented in germplasm collections. Moreover, they are under characterized and therefore grossly underutilized. The lack of in situ conservation programs further exposes them to possible genetic erosion or extinction. In order to obtain maximum benefits from these resources, it is imperative that they are collected, efficiently conserved and optimally utilized. High throughput molecular approaches such as genome sequencing could be employed to more precisely study their genetic diversity and value and thereby enhance their use in rice improvement. Oryza sativa was the first crop plant to have its reference genome sequence released marking a major milestone that opened numerous opportunities for functional characterization of the entire rice genome. Studies have however demonstrated that one reference genome sequence is not enough to fully explore the genetic variation in the Oryza genus, hence the need to have reference sequences for other species in the genus. An overview of the state of conservation and utilization of African Oryza is hereby presented. Progress in the release of reference genome sequences for these species is also highlighted.
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Affiliation(s)
- Peterson W Wambugu
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
- />Kenya Agricultural Research Institute, Nairobi, Kenya
| | - Agnelo Furtado
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
| | - Daniel LE Waters
- />Southern Cross Plant Science, Southern Cross University, Lismore, NSW Australia
| | | | - Robert J Henry
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
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Zavodna M, Grueber CE, Gemmell NJ. Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation. PLoS One 2013; 8:e61471. [PMID: 23637841 PMCID: PMC3630221 DOI: 10.1371/journal.pone.0061471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/08/2013] [Indexed: 12/02/2022] Open
Abstract
Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches - parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.
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Affiliation(s)
- Monika Zavodna
- Centre for Reproduction and Genomics, Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Catherine E. Grueber
- Centre for Reproduction and Genomics, Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
| | - Neil J. Gemmell
- Centre for Reproduction and Genomics, Department of Anatomy, University of Otago, Dunedin, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
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Abstract
Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale amplicon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Examples of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR amplicons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the above-mentioned techniques have been described.
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Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep 2012; 2:557. [PMID: 22870386 PMCID: PMC3412280 DOI: 10.1038/srep00557] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/23/2012] [Indexed: 12/25/2022] Open
Abstract
Starch is a major component of human diets. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was evaluated in a rice breeding population. Sequencing 18 genes involved in starch synthesis in a population of 233 rice breeding lines discovered 66 functional SNPs in exonic regions. Five genes, AGPS2b, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Association analysis found 31 of the SNP were associated with differences in pasting and cooking quality properties of the rice lines. Two genes appear to be the major loci controlling traits under human selection in rice, GBSSI (waxy gene) and SSIIa. GBSSI influenced amylose content and retrogradation. Other genes contributing to retrogradation were GPT1, SSI, BEI and SSIIIa. SSIIa explained much of the variation in cooking characteristics. Other genes had relatively small effects.
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Affiliation(s)
| | - Daniel L. E. Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Russell F. Reinke
- International Rice Research Institute, National Institute of Crop Science (NICS) RDA 151 Suin-ro, Gwonsun-gu, Suwon 441-857, Republic of Korea
- EH Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, NSW DPI, Private Mail Bag, Pine Gully Road, Wagga Wagga, New South Wales, 2650, Australia
| | - Rachelle Ward
- Yanco Agricultural Institute, Trunk Road 80, Yanco NSW 2703, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Qld 4072, Australia
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Hendre PS, Kamalakannan R, Varghese M. High-throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:646-56. [PMID: 22607345 DOI: 10.1111/j.1467-7652.2012.00699.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Next generation sequencing (NGS) technologies have revolutionized the pace and scale of genomics- and transcriptomics-based SNP discovery across different plant and animal species. Herein, 72-base paired-end Illumina sequencing was employed for high-throughput, parallel and large-scale SNP discovery in 41 growth-related candidate genes in Eucalyptus camaldulensis. Approximately 100 kb of genome from 96 individuals was amplified and sequenced using a hierarchical DNA/PCR pooling strategy and assembled over corresponding E. grandis reference. A total of 1191 SNPs (minimum 5% other allele frequency) were identified with an average frequency of 1 SNP/83.9 bp, whereas in exons and introns, it was 1 SNP/108.4 bp and 1 SNP/65.6 bp, respectively. A total of 75 insertions and 89 deletions were detected of which approximately 15% were exonic. Transitions (Tr) were in excess than transversions (Tv) (Tr/Tv: 1.89), but exceeded in exons (Tr/Tv: 2.73). In exons, synonymous SNPs (Ka) prevailed over the non-synonymous SNPs (Ks; average Ka/Ks ratio: 0.72, range: 0-3.00 across genes). Many of the exonic SNPs/indels had potential to change amino acid sequence of respective genes. Transcription factors appeared more conserved, whereas enzyme coding genes appeared under relaxed control. Further, 541 SNPs were classified into 196 'equal frequency' (EF) blocks with almost similar minor allele frequencies to facilitate selection of one tag-SNP/EF-block. There were 241 (approximately 20%) 'zero-SNP' blocks with absence of SNPs in surrounding ±60 bp windows. The data thus indicated enormous extant and unexplored diversity in E. camaldulensis in the studied genes with potential applications for marker-trait associations.
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Affiliation(s)
- Prasad S Hendre
- ITC R&D Centre, Peenya Industrial Area, Bangalore, Karnataka, India.
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32
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Edwards D, Henry RJ, Edwards KJ. Preface: advances in DNA sequencing accelerating plant biotechnology. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:621-2. [PMID: 22765873 DOI: 10.1111/j.1467-7652.2012.00724.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, Lee JRM, Lorenc MT, Manoli S, Stiller J, Raman R, Raman H, Edwards D, Batley J. Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:709-15. [PMID: 22726421 DOI: 10.1111/j.1467-7652.2012.00716.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A thorough understanding of the relationships between plants and pathogens is essential if we are to continue to meet the agricultural needs of the world's growing population. The identification of genes underlying important quantitative trait loci is extremely challenging in complex genomes such as Brassica napus (canola, oilseed rape or rapeseed). However, recent advances in next-generation sequencing (NGS) enable much quicker identification of candidate genes for traits of interest. Here, we demonstrate this with the identification of candidate disease resistance genes from B. napus for its most devastating fungal pathogen, Leptosphaeria maculans (blackleg fungus). These two species are locked in an evolutionary arms race whereby a gene-for-gene interaction confers either resistance or susceptibility in the plant depending on the genotype of the plant and pathogen. Preliminary analysis of the complete genome sequence of Brassica rapa, the diploid progenitor of B. napus, identified numerous candidate genes with disease resistance characteristics, several of which were clustered around a region syntenic with a major locus (Rlm4) for blackleg resistance on A7 of B. napus. Molecular analyses of the candidate genes using B. napus NGS data are presented, and the difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome are discussed.
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Affiliation(s)
- Reece Tollenaere
- Centre for Integrative Legume Research and School of Agriculture and Food Sciences, University of Queensland, Brisbane, Qld, Australia
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Bundock PC, Casu RE, Henry RJ. Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:657-67. [PMID: 22624722 DOI: 10.1111/j.1467-7652.2012.00707.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Large polyploid genomes of non-model species remain challenging targets for DNA polymorphism discovery despite the increasing throughput and continued reductions in cost of sequencing with new technologies. For these species especially, there remains a requirement to enrich genomic DNA to discover polymorphisms in regions of interest because of large genome size and to provide the sequence depth to enable estimation of copy number. Various methods of enriching DNA have been utilised, but some recent methods enable the efficient sampling of large regions (e.g. the exome). We have utilised one of these methods, solution-based hybridization (Agilent SureSelect), to capture regions of the genome of two sugarcane genotypes (one Saccharum officinarum and one Saccharum hybrid) based mainly on gene sequences from the close relative Sorghum bicolor. The capture probes span approximately 5.8 megabases (Mb). The enrichment over whole-genome shotgun sequencing was 10-11-fold for the two genotypes tested. This level of enrichment has important consequences for detecting single nucleotide polymorphisms (SNPs) from a single lane of Illumina (Genome Analyzer) sequence reads. The detection of polymorphisms was enabled by the depth of sequence at or near probe sites and enabled the detection of 270 000-280 000 SNPs within each genotype from a single lane of sequence using stringent detection parameters. The SNPs were present in 13 000-16 000 targeted genes, which would enable mapping of a large number of these chosen genes. SNP validation from 454 sequencing and between-genotype confirmations gave an 87%-91% validation rate.
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Affiliation(s)
- Peter C Bundock
- Co-operative Research Centre for Sugar Industry Innovation through Biotechnology, Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.
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