Exploring genomic structural variations for cotton crop improvement

Monika Raman, PSG College of Technology, Coimbatore

Cotton generates natural fibre for the textile industry as a commonly grown fibre crop. Thousands of enhanced cotton cultivars have contributed to increased yields. G.hirsutum is responsible for more than 90% of the total yield. On this premise, breeders try to develop new varieties by synergistically enhancing genetically complex yield and quality while acquiring resistance to a wide range of adversities. But this is limited by a lack of information on the genomic foundation of essential agronomic characteristics. 

G. Barbadense occupies approximately 10% of production and offers lint fibres of good quality. A potential strategy to enhance G.hirsutum fibres and their disease resistance are to transfer superior associated characteristics from G. barbadense into G.hirsutum; however, genetic variations in G. barbadense compared to current G. hirsutum are unclear.

Analyzing genomic structural variations for cotton improvement

The discovery of related single nucleotide polymorphisms (SNPs) provides a deeper understanding of the genetic basis of cotton agronomic features. Because of widespread genomic structural variations, such as insertion, deletion, inversion, and translocation, any single haplotype may be missing or contain sequence variants – not present in the majority of the population. 

Exploring structural variations based on genome assemblies and resequencing data from multiple accessions is necessary for cotton development. Meanwhile, the genetic effects of structural variations that underpin traits are less well understood. 

High-quality genome assembly for current G.hirsutum varieties and their obsolete types (TM-1 and ZM24) is critical for breeding and biological research. But the genomic information in recently created cotton is sparse, and the role of genomic diversity in modern breeding is unknown.

A group of researchers has uncovered many structural variations in genes and regulatory areas that influence agronomic characteristics. Their findings were published in the Nature genetics journal. 

“We produced high-quality genomes of G.hirsutum cv. NDM8 and G.barbadense acc. Pima90, and uncover large-scale structural variations in the two species and 1,081 G. hirsutum accessions,” says study lead author Zhiying Ma. 

High-quality genome assembly of modern cotton cultivars

Two high-quality assemblies of G.hirsutum cv. NDM8 and G. barbadense ac. Pima90 was produced in the current work and many genomic differences were found, interspecific and interspecific. NDM8 is widely cultivated in the Yellow River Valley cotton production areas of China. And Pima90 has contributed to serving as the genetic material in molecular breeding.

The A-subgenome of G.hirsutum had more inversions; nevertheless, the D-subgenome experienced more insertions and deletions than the A-subgenome during contemporary breeding. The structural variation density for the D-subgenome is larger than in the A-subgenome, showing that for the growth and development of species, the D-subgenome is more selected. 

Zhiying said, “We also resequenced 1,081 G.hirsutum accessions, comprising a core collection as well as numerous current and obsolete kinds with disease resistance.”

Resequencing of modern cotton cultivars

Based on sequencing G.hirsutum (TM-1, ZM24), G. barbadense (Hai7124, 3-79), and resequencing accessions numerous publications regarding the genomic diversity of Gossypium allopolyploid species have been published. 

They discovered that 15,973 genes could belong to duplicates and alleles of few genes in tetraploid cotton, and 80,992 genes were nonredundant in the six genomes, providing new information for plant genome researchers.

For crop improvement

They concluded that, out of 446 structural variants, the ones for fibre quality and the resistance to Verticillium wilt are predominantly found in the D-subgenome and those for yield, especially the A-subgenome. 

Analysis of these two genomes and resequences has shown that substantial genomic differences occur inbreeding that provides resources for the development of cotton crops. These shed light on the relevance of structural variations in genotype-to-phenotype connections, as well as their potential for crop development.

Also read: Goodpasture Syndrome- A Condition affecting One in every Million

Reference Ma, Z., Zhang, Y., Wu, L., Zhang, G., Sun, Z., Li, Z., Jiang, Y., Ke, H., Chen, B., Liu, Z., Gu, Q., Wang, Z., Wang, G., Yang, J., Wu, J., Yan, Y., Meng, C., Li, L., Li, X., … Wang, X. (2021). High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. Nature Genetics, 1–7. https://doi.org/10.1038/s41588-021-00910-2

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About the author: Monika Raman is an undergraduate student pursuing her final year B. Tech in Biotechnology. She is an enthusiastic Biotech student aspiring for an opportunity to develop skills and grow professionally in the research field. Extremely motivated and possess strong interpersonal skills.