Integrated meta‐QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.)

• Published in: The plant genome 2024-09, Vol.17 (3), p.e20492-n/a
• Main Authors: Yang, Changgang, Zhang, Xueting, Wang, Shihong, Liu, Na
• Format: Article
• Language: English
• Subjects: Agricultural production; allelic variation; Chromosome Mapping; Climate change; Computer Simulation; confidence interval; Crop yield; Food; Genes; Genetic analysis; Genetic linkage; Genome, Plant; Genomes; genomics; Haplotypes; Homology; Independent study; loci; marker-assisted selection; Morphology; Nitrogen; Plant breeding; Polymerase chain reaction; Polymorphism; Polymorphism, Single Nucleotide; Population; Quantitative Trait Loci; Rice; Single-nucleotide polymorphism; Transcriptome; Transcriptomes; Transcriptomics; Triticum - genetics; Triticum aestivum; Wheat
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20492

Spike length (SL) is one of the major contributors to wheat yield. Uncovering major genetic regions affecting SL is an integral part of elucidating the genetic basis of wheat yield traits and goes further pivotal for marker‐assisted selection breeding. A genome‐wide meta‐quantitative trait locus (MQTL) analysis of wheat SL resulted in the refinement of 48 MQTLs using 227 initial QTLs retrieved from previous studies published over the past decades. The average confidence interval (CI) of these MQTLs amounted to a 5.16‐fold reduction compared to the mean CI of the initial QTLs. As many as 2240 putative candidate genes (CGs) were identified from the MQTL intervals using transcriptomics data in silico of wheat, of which 58 CGs were identified based on wheat–rice homology analysis. For the key CG affecting SL, a functional kompetitive allele‐specific PCR (KASP) marker, TaPP2C‐3B‐KASP, was developed to distinguish TaPP2C‐3B‐Hap I and TaPP2C‐3B‐Hap II based on the single nucleotide polymorphism at the 272 bp (A/G). The frequency of the elite allelic variation TaPP2C‐3B‐Hap II with high SL remained relatively stable at about 49.62% from the 1960s to 1990s. Integration of MQTL analysis and in silico transcriptome data led to a significant increase in the reliability of CGs for the genetic regulation of wheat SL, and the haplotype analysis for key CGs TaPP2C‐3B of SL provided insights into the biological function of the TaPP2C‐3B gene. Core Ideas As many as 227 initial quantitative trait loci (QTLs) related to spike length (SL) were collected to conduct the meta‐QTL (MQTL) analysis. The 48 MQTLs which harbored 2240 putative candidate genes (CGs) were identified. A functional kompetitive allele‐specific PCR (KASP) marker was developed for TaPP2C‐3B. The haplotype TaPP2C‐3B‐Hap II was an elite allelic variation for high SL. Plain Language Summary Uncovering major genomic regions affecting spike length (SL) is an integral part of illustrating the genetic basis of wheat yield traits. In the current study, a meta‐analysis for wheat SL on the basis of 227 initial quantitative trait loci (QTLs) published in the previous studies was performed to mine key candidate genes (CGs). The 48 meta‐QTL (MQTLs) which harbored 2240 putative CGs were identified. A functional kompetitive allele‐specific PCR marker was developed for the critical gene TaPP2C‐3B and the haplotype TaPP2C‐3B‐Hap II was favorable for improving SL. Integration of MQTL analysis and in silico transcriptome data a