Genomics, Pan-Genomics, and Super Pan-Genomics of Major Oilseed Crops

Edited book (chapter)

Naik, Yogesh Dashrath, Rangari, Sagar Krushnaji, Garcia-Caparros, Pedro, Jan, Farkhandah, Gangurde, Sunil Shiwaji, Zwart, Rebecca, Aski, Muraleedhar S., Mendu, Venugopal, Jha, Uday, Elango, Dinakaran, Pandey, Manish K., Mir, Reyazul Rouf, Varshney, Rajeev, Punnuri, Somashekhar M. and Thudi, Mahendar. 2025. "Genomics, Pan-Genomics, and Super Pan-Genomics of Major Oilseed Crops." Pandey, Manish K, Mallikarjuna, M. G., Lohithaswa, H. C., Aski, Muraleedhar S. and Gupta, Sanjeev (ed.) Breeding Climate Resilient and Future Ready Oilseed Crops. Singapore. Springer. pp. 7-41
Chapter Title

Genomics, Pan-Genomics, and Super Pan-Genomics of Major Oilseed Crops

Book Chapter CategoryEdited book (chapter)
ERA Publisher ID3337
Book TitleBreeding Climate Resilient and Future Ready Oilseed Crops
AuthorsNaik, Yogesh Dashrath, Rangari, Sagar Krushnaji, Garcia-Caparros, Pedro, Jan, Farkhandah, Gangurde, Sunil Shiwaji, Zwart, Rebecca, Aski, Muraleedhar S., Mendu, Venugopal, Jha, Uday, Elango, Dinakaran, Pandey, Manish K., Mir, Reyazul Rouf, Varshney, Rajeev, Punnuri, Somashekhar M. and Thudi, Mahendar
EditorsPandey, Manish K, Mallikarjuna, M. G., Lohithaswa, H. C., Aski, Muraleedhar S. and Gupta, Sanjeev
Page Range7-41
Chapter Number2
Number of Pages35
Year2025
PublisherSpringer
Place of PublicationSingapore
ISBN9789819777433
9789819777440
Digital Object Identifier (DOI)https://doi.org/10.1007/978-981-97-7744-0_2
Web Address (URL)https://link.springer.com/chapter/10.1007/978-981-97-7744-0_2
Abstract

Oilseed crops, such as soybean, groundnut, mustard, sunflower, and sesame, are important in global agriculture due to human consumption and industrial applications. Considering their importance in global agriculture, there has been significant attention given to improving both seed oil content and quality. Oil synthesis and accumulation are regulated by complex biochemical pathways and are typically classified as quantitative traits. Over the past few decades, the elucidation of regulatory pathways governing fatty acid synthesis, identification of target genes and advancements in metabolic engineering have made significant progress. Additionally, advancements in sequencing technologies and revolutionized bioinformatics have helped in a significant transformation in the field of genomic analysis. This transformation involves a shift from analyzing individual cultivars to encompassing studies of entire species at the genomic level. This paradigm shift is aimed at comprehensively capturing the full spectrum of diversity. This chapter explores the complexities of traits linked to oil content and recent advancements in mapping these traits to gain a deeper understanding of their complexity. Additionally, the concepts of the pan-genome and super pan-genome, along with the methods employed for their construction are discussed. We also discuss the current challenges faced in major oilseed crops and consider the future prospects for this ever-evolving field.

KeywordsOilseeds; Sequencing; Genomics; Pan-genome; Crop improvement; Structural variation
Contains Sensitive ContentDoes not contain sensitive content
ANZSRC Field of Research 2020310509. Genomics
300406. Crop and pasture improvement (incl. selection and breeding)
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Byline AffiliationsDr. Rajendra Prasad Central Agricultural University, India
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
University of Almeria, Spain
Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), India
Centre for Crop Health
Indian Agricultural Research Institute, India
Texas A&M University, United States
Indian Council of Agricultural Research-Indian Institute of Pulses Research (IIPR), India
Iowa State University, United States
Murdoch University
Dr. Fort Valley State University, United States
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Zwart, Rebecca S., Muylle, Hilde, Van Bockstaele, Erik and Roldán-Ruiz, Isabel. 2008. "Evaluation of genetic diversity of Fusarium head blight resistance in European winter wheat." Theoretical and Applied Genetics: international journal of plant breeding research. 117 (5), pp. 813-828. https://doi.org/10.1007/s00122-008-0822-3
Combining ability analysis of Fusarium head blight resistance in western European wheat lines
Zwart, Rebecca S., Muylle, Hilde, Van Huylenbroeck, Johan, Van Bockstaele, Erik and Roldán-Ruiz, Isabel. 2008. "Combining ability analysis of Fusarium head blight resistance in western European wheat lines." Euphytica: international journal on plant breeding. 162 (3), pp. 449-456. https://doi.org/10.1007/s10681-007-9611-3
Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population
Zwart, R. S., Thompson, J. P., Sheedy, J. G. and Nelson, J.. 2006. "Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population." Australian Journal of Agricultural Research. 57 (5), pp. 525-530. https://doi.org/10.1071/AR05177
Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat
Zwart, R. S., Thompson, J. P. and Godwin, I. D.. 2005. "Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat ." Australian Journal of Agricultural Research. 56 (4), pp. 345-352. https://doi.org/10.1071/AR04223
Genetic analysis of resistance to root-lesion nematode (Pratylenchusthornei) in wheat
Zwart, R. S., Thompson, J. P. and Godwin, I. D.. 2004. "Genetic analysis of resistance to root-lesion nematode (Pratylenchusthornei) in wheat." Plant Breeding. 123 (3), pp. 209-212. https://doi.org/10.1111/j.1439-0523.2004.00986.x
Inheritance and mapping of 11 avirulence genes in Phytophthora sojae
May, K.J., Whisson, S.C., Zwart R.S., Searle, I.R., Irwin, J.A.G., Maclean, D.J., Carroll, B.J. and Drenth, A.. 2002. "Inheritance and mapping of 11 avirulence genes in Phytophthora sojae ." Fungal Genetics and Biology. 37 (1), pp. 1-12. https://doi.org/10.1016/S1087-1845(02)00027-0