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RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

X-linked Traits

X-linked Traits

In most mammalian species, females have two X sex chromosomes and males have an X and Y. As a result, mutations on the X chromosome in females may be masked by the presence of a normal allele on the second X. In contrast, a mutation on the X chromosome in males more often causes observable biological defects, as there is no normal X to compensate. Trait variations arising from mutations on the X chromosome are called “X-linked”.

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Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts

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Mapping intron retention events contributing to complex traits using splice quantitative trait locus.

Siyuan Wang¹, Hongyu Wu¹, Yongyan Zhao^1,2

¹Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China.

|July 21, 2023

Summary

This summary is machine-generated.

Alternative splicing impacts crop yield. Splice quantitative trait loci (sQTLs) are identified as novel genetic resources for precision cotton breeding, aiding in yield and quality improvements.

Keywords:

Alternative splicing (AS)Cotton (Gossypium hirsutum L.)Fiber yield Intron retention (IR)Splicing quantitative trait locus (sQTL)

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Area of Science:

Plant genetics
Molecular biology
Agronomy

Background:

Alternative splicing (AS) of mRNA is crucial for transcriptome diversity and regulates plant growth and stress responses.
Understanding AS variations in crop populations offers insights into complex agronomic traits.
Genome-wide association studies (GWAS) on AS events in crops are limited.

Purpose of the Study:

To develop a pipeline for identifying candidate AS events linked to complex traits in upland cotton.
To investigate the role of AS, specifically intron retention (IR), in regulating cotton fiber yield and quality.

Main Methods:

Genome-wide characterization of intron retention (IR) in an upland cotton population (279 lines) using ovule transcriptome data.
Splice quantitative trait locus (sQTL) analysis to identify genetic variants associated with AS events.
Integration of sQTL analysis with expression quantitative trait loci (eQTL) and GWAS loci.

Main Results:

A total of 2295 sQTLs involving 1607 genes were identified, with 14.25% being cis-regulatory.
53% of cis-sGenes were co-regulated by cis-sQTLs and cis-eQTLs.
32 cis-QTLs co-localized with GWAS loci for fiber yield and quality traits, suggesting their regulatory role.
Differential IR rates in genes like GhLRRK1 and GhGC1 correlated with lint percentage (LP).

Conclusions:

Alternative splicing significantly impacts crop yield and quality traits.
Functional sQTLs represent valuable genetic resources for precision breeding in cotton.
Identified AS events and associated genes offer potential for improving cotton fiber traits.