Role of SNPs in determining QTLs for major traits in cotton

Authors: MAJEED, SAJID - Pakistan University Of Agriculture; RANA, IQRAR AHMAD - Pakistan University Of Agriculture; ATIF, RANA MUHAMMAD - Pakistan University Of Agriculture; ALI, ZULFIQAR - Muhammad Nawaz Shareef University Of Agriculture; Hinze, Lori; AZHAR, M TEHSEEN - Pakistan University Of Agriculture

Submitted to: Journal of Cotton Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2019
Publication Date: 5/29/2019
Citation: Majeed, S., Rana, I., Atif, R., Ali, Z., Hinze, L.L., Azhar, M. 2019. Role of SNPs in determining QTLs for major traits in cotton. Journal of Cotton Research. 2:5. https://doi.org/10.1186/s42397-019-0022-5.
DOI: https://doi.org/10.1186/s42397-019-0022-5

Interpretive Summary: Recent advances in the identification of small variations in cotton genomes have led to the increased use of these variations in genetics research programs. This use spans a range of applications for plant traits including fiber quality and yield, tolerance to drought and disease stress, as well as characters important for plant development. In an effort to condense this information, a literature review was conducted to summarize published accounts specifically about how these small variations have been used to identify larger genetic regions important in cotton breeding programs. The results of this review are important to other scientists working in cotton in that applications of these genetic variations have been identified so future avenues of research can be identified and build upon previous research.

Technical Abstract: Single nucleotide polymorphism is the simplest form of genetic variation among individuals that induce minor changes in phenotypic, physiological and biochemical characteristics. It induces various types of mutations which are involved in alteration of the sequence of a gene; in fact, changes are observed in amino acids. The changes in yield related traits have more concerns to plant breeders. Several assays for identification and validation of these markers have been developed and later on these are evaluated in crop plants. Each method has its own pros and cons but genotyping by sequencing is the common and widely used assay for the identification of superior traits of interest. These markers are also associated with several desirable traits like yield, fibre quality, boll size and genes respond to biotic and abiotic stresses in cotton. Numerous quantitative trait loci with novel functions have been identified in cotton by using these markers. This information can be used for crop improvement through molecular breeding approaches. In this review, we discussed the identification of these markers and their effects on gene function of economically important traits in cotton.