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E-book: Genotyping by Sequencing for Crop Improvement

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  • Pub. Date: 29-Mar-2022
  • Publisher: John Wiley & Sons Inc
  • Language: eng
  • ISBN-13: 9781119745662
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Genotyping by Sequencing for Crop ImprovementLarger Image
  • Format: PDF+DRM
  • Pub. Date: 29-Mar-2022
  • Publisher: John Wiley & Sons Inc
  • Language: eng
  • ISBN-13: 9781119745662
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"Recent advances in sequencing technology has brought numerous opportunities for several domains of science focusing on basic as well as applied research. Plant genomics is one such domain where the shift of paradigm has been witnessed more evidently. Genotyping by sequencing (GBS) has become an indispensable tool for the plant science community. There are numerous advances making GBS more efficient for specific crops. Several technological and analytical options are available with GBS. Now, GBS is beingused for day to day breeding activities, germplasm screening, diagnostic application, and basic research"--

OGENOTYPING BY SEQUENCING FOR CROP IMPROVEMENT

A thoroughly up-to-date exploration of genotyping-by-sequencing technologies and related methods in plant science

In Genotyping by Sequencing for Crop Improvement, a team of distinguished researchers delivers an in-depth and current exploration of the latest advances in genotyping-by-sequencing (GBS) methods, the statistical approaches used to analyze GBS data, and its applications, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) in crop improvement. This edited volume includes insightful contributions on a variety of relevant topics, like advanced molecular markers, high-throughput genotyping platforms, whole genome resequencing, QTL mapping with advanced mapping populations, analytical pipelines for GBS analysis, and more.

The distinguished contributors explore traditional and advanced markers used in plant genotyping in extensive detail, and advanced genotyping platforms that cater to unique research purposes are discussed, as is the whole-genome resequencing (WGR) methodology. The included chapters also examine the applications of these technologies in several different crop categories, including cereals, pulses, oilseeds, and commercial crops. Genotyping by Sequencing for Crop Improvement also offers:

  • A thorough introduction to molecular marker techniques and recent advancements in the technology
  • Comprehensive explorations of the genotyping of seeds while preserving their viability, as well as advances in genomic selection
  • Practical discussions of opportunities and challenges relating to high throughput genotyping in polyploid crops
  • In-depth examinations of recent advances and applications of GBS, GWAS, and GS in cereals, pulses, oilseeds, millets, and commercial crops

Perfect for practicing plant scientists with an interest in genotyping-by-sequencing technology, Genotyping by Sequencing for Crop Improvement will also earn a place in the libraries of researchers and students seeking a one-stop reference on the foundational aspects of – and recent advances in – genotyping-by-sequencing, genome-wide association studies, and genomic selection.

List of Contributors xv
Preface xix
1 Molecular Marker Techniques and Recent Advancements 1(21)
Dharminder Bhatia
Gagandeep Singh Bajwa
1.1 Introduction
1(1)
1.2 What is a Molecular Marker?
2(1)
1.3 Classes of Molecular Markers
2(5)
1.3.1 Hybridization-based Markers
2(1)
1.3.1.1 Restriction Fragment Length Polymorphism (RFLP)
2(1)
1.3.1.2 Diversity Array Technology (DArTTM)
3(1)
1.3.2 Polymerase Chain Reaction (PCR)-based Markers
3(4)
1.3.2.1 Simple-Sequence Repeats (SSRs)
3(1)
1.3.2.2 Sequence-Tagged Sites (STSs)
4(1)
1.3.2.3 Randomly Amplified Polymorphic DNAs (RAPDs)
4(2)
1.3.2.4 Sequence Characterized Amplified Regions (SCARS)
6(1)
1.3.2.5 Amplified Fragment Length Polymorphism (AFLP)
6(1)
1.3.2.6 Expressed Sequence Tags (ESTs)
6(1)
1.4 Sequencing-based Markers
7(1)
1.4.1 Single-Nucleotide Polymorphisms (SNPs)
7(1)
1.4.2 Identification of SNP in a Pregenomic Era
7(1)
1.5 Recent Advances in Molecular Marker Technologies
7(5)
1.5.1 Genotyping-by-Sequencing (GBS)
8(1)
1.5.2 Whole-Genome Resequencing (WGR)
9(1)
1.5.3 SNP Arrays
10(1)
1.5.4 Kompetitive Allele-Specific PCR (KASP™)
11(1)
1.6 SNP Databases
12(1)
1.7 Application of Molecular Markers
13(2)
1.7.1 Application of Molecular Markers in Crop Improvement
13(1)
1.7.2 Role of Molecular Markers in Germplasm Characterization
14(1)
1.7.3 Deployment of Molecular Markers in Plant Variety Protection and Registration
14(1)
1.8 Summary
15(1)
References
15(7)
2 High-throughput Genotyping Platforms 22(16)
Sandhya Sharma
Kuldeep Kumar
Kishor Tribhuvan
Rita
Sandeep Kumar
Priyanka Jain
Swati Saxena
Joshita Vijayan
Harsha Srivastava
Kishor Gaikwad
2.1 Introduction
22(1)
2.2 SNP Genotyping Platforms
23(12)
2.2.1 SNP Genotyping Versus SNP Discovery
23(1)
2.2.2 Types of SNP Genotyping Platforms
24(10)
2.2.2.1 Allelic Discrimination
24(6)
2.2.2.2 Allelic Detection
30(4)
2.2.3 Custom Assay Technologies
34(1)
2.2.4 Summary
34(1)
References
35(3)
3 Opportunity and Challenges for Whole-Genome Resequencing-based Genotyping in Plants 38(14)
Surbhi Kumawat
Gaurav Raturi
Pallavi Dhiman
Sreeja Sudhakarn
Nitika Rajora
Vandana Thakral
Himanshu Yadav
Gunashri Padalkar
Yogesh Sharma
Vinaykumar Rachappanavar
Manish Kumar
3.1 Introduction
38(2)
3.2 Basic Steps Involved in Whole-Genome Sequencing and Resequencing
40(1)
3.3 Whole-Genome Resequencing Mega Projects in Different Crops
41(2)
3.3.1 1K Arabidopsis Genomes Resequencing Project
41(1)
3.3.2 3K Rice Genomes Resequencing Project
41(1)
3.3.3 Soybean Whole-Genome Resequencing
42(1)
3.3.4 Chickpea
42(1)
3.3.5 Pigeon pea
42(1)
3.3.6 Vitis
43(1)
3.4 Whole-Genome Pooled Sequencing
43(1)
3.5 Pinpointing Gene Through Whole-Genome Resequencing-based QTL Mapping
44(1)
3.6 Online Resources for Whole-Genome Resequencing Data
45(1)
3.6.1 SNP Seek
45(1)
3.6.2 Rice Functional and Genomic Breeding
45(1)
3.6.3 Genome Variation Map
45(1)
3.7 Applications and Successful Examples of Whole-Genome Resequencing
45(1)
3.8 Challenges for Whole-Genome Resequencing Studies
46(2)
3.9 Summary
48(1)
References
48(4)
4 QTL Mapping Using Advanced Mapping Populations and High-throughput Genotyping 52(28)
Sweta Sinha
Brij Kishore Kushwaha
Rupesh K. Deshmukh
4.1 Introduction
52(1)
4.2 The Basic Objectives of QTL Mapping
53(1)
4.3 QTL Mapping Procedure
53(1)
4.4 The General Steps for QTL Mapping
53(1)
4.5 Factors Influencing QTL Analysis
53(1)
4.6 QTL Mapping Approaches
54(3)
4.7 Statistical Methods for QTL Mapping
57(4)
4.8 Software for QTL Mapping
61(1)
4.9 Bi-parental Mapping Populations
61(2)
4.10 QTL Mapping Using Bi-parental Populations
63(1)
4.11 Multiparental Mapping Populations
64(1)
4.11.1 Nested Association Mapping (NAM)
64(1)
4.11.2 Multi-advanced Generation Inter-cross Populations (MAGIC)
65(1)
4.12 QTL Mapping Using Multiparental Populations
65(1)
4.13 Use of High-throughput Genotyping for QTL Mapping
66(3)
4.13.1 PCR-based SNP Genotyping
67(2)
4.14 Next-Generation Sequencing-based Genotyping
69(3)
4.14.1 Restriction-Site-Associated DNA Sequencing (RAD-seq)
69(1)
4.14.2 Genotyping-by-Sequencing
69(1)
4.14.3 Whole-Genome Resequencing
70(2)
4.15 Challenges with QTL Mapping Using Multiparental Populations and High-throughput Genotyping
72(1)
References
72(8)
5 Genome-Wide Association Study: Approaches, Applicability, and Challenges 80(32)
Akshay S. Sakhare
Suneetho Kota
Santosh Rathod
Brajendra Parmar
Viswanathan Chinnusomy
5.1 Introduction
80(1)
5.2 Methodology to Conduct GWAS in Crops
81(3)
5.3 Statistical Modeling in GWAS
84(1)
5.4 Efficiency of GWAS with Different Marker Types
85(1)
5.5 Computational Tools for GWAS
86(1)
5.6 GWAS Challenges for Complex Traits
86(1)
5.7 Factors Challenging the GWAS for Complex Traits
87(1)
5.8 GWAS Applications in Major Crops
88(10)
5.8.1 Maize
88(4)
5.8.2 Rice
92(2)
5.8.3 Wheat
94(1)
5.8.4 Barley
95(2)
5.8.5 Pearl Millet
97(1)
5.8.6 Sugarcane
98(1)
5.9 Candidate Gene Identification at GWAS Loci
98(3)
5.10 Meta-GWAS
101(1)
5.11 GWAS vs. QTL Mapping
102(1)
References
102(10)
6 Genotyping of Seeds While Preserving Their Viability 112(29)
Vinaykumar Rachappanavar
Arushi Padiyal
Jitender Kumar Sharma
6.1 Introduction
112(4)
6.1.1 Genotyping
114(1)
6.1.2 Genotyping-by-Sequencing
115(1)
6.2 Genotyping-by-Sequencing with Minimum DNA
116(1)
6.3 DNA Extraction from Half Grain
117(5)
6.3.1 DNA Extraction from Rice Seeds
119(1)
6.3.2 DNA Extraction from Wheat and Barley Seeds
120(1)
6.3.3 DNA Extraction from Maize Seeds
120(1)
6.3.4 DNA Extraction from Soybean Seeds
121(1)
6.3.5 DNA Extraction from Cotton Seeds
121(1)
6.3.6 DNA Extraction from Papaya Seeds
121(1)
6.3.7 DNA Extraction from Watermelon Seeds
122(1)
6.4 GBS with Half Seed
122(3)
6.5 Applications of GBS as Diagnostic Tool
125(4)
6.5.1 Germplasm Conservation and Quality Control
125(1)
6.5.2 Tracking Crop Varieties
126(1)
6.5.3 Sex Determination
126(2)
6.5.4 Transgenic Detection
128(1)
6.5.5 Detection of Seed-borne Diseases
128(1)
6.6 Summary
129(1)
References
129(12)
7 Genomic Selection: Advances, Applicability, and Challenges 141(20)
Naina Garewal
Riya Joon
Ravneet Kaur
Kashmir Singh
7.1 Introduction
141(1)
7.2 Natural Selection
142(1)
7.3 Breeding Selection
143(1)
7.4 Marker-assisted Selection
144(1)
7.5 Genomic Selection
145(2)
7.6 Genotyping for Genomic Selection
147(3)
7.7 Integration of Genomic Selection in MAS Program
150(1)
7.8 The Efficiency of Genomic Selection for Complex Traits
150(2)
7.9 Integration of Genomic Selection in the Varietal Trial Program
152(3)
7.10 Cost Comparison of GS vs MAS
155(1)
References
155(6)
8 Analytical Pipelines for the GBS Analysis 161(27)
Vinaykumar Rachappanavar
Arushi Padiyal
Jitender Kumar Sharma
Narender Negi
8.1 Introduction
161(3)
8.2 Applications of NGS
164(1)
8.3 NGS Sequencing Platforms
164(3)
8.3.1 Sequencing by Synthesis
164(1)
8.3.1.1 Roche 454 Pyrosequencing
164(1)
8.3.1.2 Illumina
165(1)
8.3.1.3 Ion Torrent
165(1)
8.3.2 Sequencing by Ligation
165(1)
8.3.2.1 SOLiD
165(1)
8.3.2.2 Polonator
165(1)
8.3.3 Single-Molecule Sequencing
166(5)
8.3.3.1 Helicos
166(1)
8.3.3.2 Pacific Bioscience
166(1)
8.3.3.3 ChIP-Sequencing
167(1)
8.4 Tools for NGS Data Analysis
167(4)
8.5 Generalized Procedure for NGS Data Analysis
171(4)
8.5.1 Assessment of Quality
172(2)
8.5.2 Aligning Sequences
174(1)
8.5.3 Identification of Variants
174(1)
8.6 Variant Annotation
175(1)
8.6.1 Visualization of NGS Data
175(1)
8.7 Role of NGS Informatics in Identifying Variants
175(1)
8.8 Genotyping by Sequencing
176(1)
8.9 Analytical Pipelines for GBS
176(4)
8.10 Comparison of GBS Pipelines
180(1)
References
181(7)
9 Recent Advances and Applicability of GBS, GWAS, and GS in Maize 188(30)
Anshuman Tiwari
Shalu Choudhary
Jayendra Padiya
Abhijit Ubale
Venugopal Mikkilineni
Bharat Char
9.1 Introduction
188(1)
9.2 Maize Genetics
189(1)
9.3 Importance of Genomics and Genotyping-based Applications in Maize Breeding Programs
190(1)
9.4 GBS-based QTL Mapping in Maize
191(8)
9.5 GBS Protocols and Analytical Pipelines for Maize
199(2)
9.6 Maize Genome Sequencing and Resequencing
201(1)
9.6.1 Maize Resequencing
201(1)
9.7 Genotyping-by-Sequencing-based GWAS and GS Efforts in Maize
202(7)
9.8 Summary
209(1)
References
210(8)
10 Recent Advances and Applicability of GBS, GWAS, and GS in Soybean 218(32)
Prashant Raghunath Shingote
Dhananjay Narayanrao Gotarkar
Ravindra Ramrao Kale
Omkar Maharudra Limbalkar
Dhiraj Lalji Wasule
10.1 Introduction
218(3)
10.1.1 Importance of Soybean for Global Food Security
218(2)
10.1.2 Challenges in Soybean Production
220(1)
10.1.3 Soybean Genetic Improvement
221(1)
10.2 GBS Efforts in Soybean
221(1)
10.3 High-Density Linkage Maps in Soybean
222(3)
10.4 GBS Protocols and Analytical Pipelines for Soybean
225(2)
10.5 GBS-based QTL Mapping Efforts in Soybean
227(3)
10.6 Soybean Genome Sequencing and Resequencing
230(3)
10.7 GBS-based GWAS Efforts in Soybean
233(7)
10.7.1 The General Procedure for Association Mapping
233(1)
10.7.2 Approaches Used for Association Studies
234(6)
10.8 GBS-based Genomic Selection Efforts in Soybean
240(3)
References
243(7)
11 Advances and Applicability of Genotyping Technologies in Cotton Improvement 250(20)
Shubham Bhardwaj
Vikas Devkar
Amit Kumar
Alish Alisha
Shivani Sharma
Rupesh K. Deshmukh
Gunvant B. Patil
11.1 Introduction
250(1)
11.2 Challenges due to Polyploidy in Cotton
251(1)
11.3 Applications of Genomics and Genotyping for Cotton Breeding Programs
251(2)
11.4 Genotyping Efforts in Cotton
253(2)
11.5 High-Density Linkage Maps in Cotton
255(2)
11.6 Whole-Genome Sequencing of Cotton Germplasm
257(2)
11.7 Application of GBS Technology in Cotton Research
259(1)
11.8 GBS-based Bi-Parental QTL Mapping and Association Mapping in Cotton
260(2)
11.9 Summary and Outlook
262(1)
References
262(8)
12 Recent Advances and Applicability of GBS, GWAS, and GS in Millet Crops 270(25)
Pankaj S. Mundada
Swapnil B. Kadam
Anupama A. Pable
Vitthal T. Barvkar
12.1 Introduction
270(2)
12.2 GBS Efforts in Millet Crops
272(3)
12.3 High-density Linkage Maps in Millet Crops
275(2)
12.4 GBS-based QTL Mapping Efforts in Millet Crops
277(3)
12.5 Genome Sequencing and Resequencing of Millet Crops
280(5)
12.5.1 Pearl Millet
281(1)
12.5.2 Broomcorn Millet
281(1)
12.5.3 Finger Millet
282(1)
12.5.4 Foxtail Millet
282(1)
12.5.5 Sorghum
283(2)
12.6 GBS-based GWAS Efforts in Millet Crops
285(2)
12.7 GBS-based Genomic Selection (GS) Efforts in Millet Crops
287(3)
12.8 Summary
290(1)
References
290(5)
13 Recent Advances and Applicability of GBS, GWAS, and GS in Pigeon Pea 295(11)
Anuradha Singh
Nisha Singh
13.1 Introduction
295(1)
13.2 Pigeon Pea Sequencing and Resequencing
296(1)
13.3 Development of Pigeon Pea High-density Genotyping Platforms
297(1)
13.4 Development of High-density Linkage Maps in Pigeon Pea
297(2)
13.5 QTL Analysis Using High-density Genotyping Platforms and GBS
299(1)
13.6 GWAS Efforts in Pigeon Pea
299(3)
13.7 Genomic Selection (GS) Efforts in Pigeon Pea
302(1)
13.8 Summary
302(1)
References
303(3)
14 Opportunity and Challenges for High-throughput Genotyping in Sugarcane 306(22)
Prathima P. Thirugnanasambandam
Avinash Singode
Lakshmipathy Thalambedu
Senthilkumar Shanmugavel
14.1 Introduction
306(1)
14.2 Sugarcane Genome and Genetics
307(1)
14.3 Genetic Studies and Marker Systems
308(1)
14.4 Genotyping-by-Sequencing (GBS)
309(3)
14.5 SNP Calling Using GBS Pipelines
312(1)
14.6 Sugarcane Genome Sequencing
313(2)
14.7 Linkage and QTL Mapping in Sugarcane
315(3)
14.8 GWAS in Sugarcane
318(2)
14.9 Genomic Selection in Sugarcane
320(2)
14.10 Summary
322(1)
References
322(6)
15 Recent Advances and Applicability of GBS, GWAS, and GS in Polyploid Crops 328(27)
Vandana Thakral
Himanshu Yadav
Gunashri Padalkar
Surbhi Kumawat
Gaurav Raturi
Virender Kumar
Rushil Mandlik
Nitika Rajora
Manipal Singh
15.1 Introduction
328(1)
15.2 Challenges for Genotyping in Polyploidy Crops
329(1)
15.3 Genotyping Platforms for Barley
330(1)
15.4 Long-Read Sequencing-based Genotyping in Polyploid Canola
331(2)
15.5 Peanut Genotyping with Targeted Amplicon Sequencing
333(1)
15.6 SNP Genotyping Methods and Platforms Available for Sugarcane
334(2)
15.7 Recent Advances and Applicability of GBS, GWAS, and GS in Polyploidy Crop Species
336(2)
15.7.1 Linkage Maps and Mapping Software Tools for Polyploids
336(2)
15.8 Haplotype-based Genotyping
338(1)
15.9 GBS Analytical Pipelines for Polyploids
339(1)
15.9.1 Fast-GBS
339(1)
15.9.2 Po1yRAD
339(1)
15.9.3 UGbS-Flex
339(1)
15.9.4 HaploTag
340(1)
15.10 GBS-based QTL Mapping Efforts in Polyploids
340(3)
15.10.1 Wheat
341(1)
15.10.2 Potato
341(1)
15.10.3 Sugarcane
342(1)
15.10.4 Canola
342(1)
15.10.5 Peanut
343(1)
15.10.6 Cotton
343(1)
15.11 GWAS and GS Using High-throughput Genotyping in Polyploidy Crops
343(2)
15.11.1 Wheat
344(1)
15.11.2 Potato
344(1)
15.11.3 Sugarcane
344(1)
15.11.4 Canola
344(1)
15.11.5 Peanut
345(1)
15.11.6 Cotton
345(1)
References
345(10)
16 Recent Advances and Applicability of GBS, GWAS, and GS in Oilseed Crops 355(16)
Sanskriti Vats
Yogesh Sharma
Virender Kumar
Rushil Mandlik
Surbhi Kumawat
Himonshu Yadav
Pallavi Dhiman
Vandana Thakral
Md Aminul Islam
Sreeja Sudhakaran
16.1 Introduction
355(1)
16.2 GBS Efforts in Oilseed Crops
356(1)
16.3 High-density Linkage Maps for Oilseed Crops
357(3)
16.3.1 High-density Linkage Maps for Peanut
357(1)
16.3.2 High-density Linkage Maps for Sunflower
358(1)
16.3.3 High-density Linkage Maps of Sesamum
358(1)
16.3.4 High-density Linkage Maps of Safflower
359(1)
16.3.5 High-density Linkage Maps of Linseed
359(1)
16.3.6 High-density Linkage Maps of Soybean
359(1)
16.3.7 High-density Linkage Maps of Rapeseed
360(1)
16.4 GBS Protocols and Analytical Pipelines
360(1)
16.5 GBS-based QTL Mapping Efforts in Oilseed Crops
361(4)
16.5.1 GBS-based QTL in Peanut
361(3)
16.5.2 GBS-based QTL in Soybean
364(1)
16.5.3 GBS-based QTL in Rapeseed
364(1)
16.6 GBS-based GWAS Efforts in Oilseed Crops
365(2)
References
367(4)
Index 371
Humira Sonah, National Agri-Food Biotechnology Institute, Punjab, India



Vinod Goyal, CCS Haryana Agriculture University, Hisar, India

S. M. Shivaraj, Laval University, Quebec City, Canada

Rupesh K. Deshmukh, Ramalingaswami Fellow, National Agri-Food Biotechnology Institute, Punjab, India
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