Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment

Abstract

Background Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement. Results With the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat. Conclusions The findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.

Natural allelic variation confers diversity in the regulation of flag leaf traits in wheat

“…Cultivars from Central and Northern Europe showed higher values for FLW and FLA compared to North American and Eastern Europe-Western Asia accessions. Extensive phenotypic variation among these traits has been widely reported mainly in DH and RIL populations 16 , 22 and diverse panels 17 , 30 , however, an association on the genotype´s origin as described here has not been previously documented. Future studies should assess if differences in FL dimensions are related to an indirect selection effect concerning the photosynthetic active radiation available at different latitudes.…”

“…As previously reported, flag leaf morphological traits are quantitative traits controlled by multiple genes 6 , 65 . Recently some authors have compiled previous reports related to QTL involved in flag morphological traits on different wheat chromosomes 22 , 65 . Even though previous efforts mainly using RILs and DH population have documented markers linked with flag leaf morphology on 1A 22 , 1B 19 , 36 , 2A, 19 , 2B 19 , 3A 36 , 3B 22 , 4A 22 , 4B 22 , 5A 19 , 36 , 5B 19 , 6B 36 , 7A 22 , 7B and 7D 36 , those QTNs documented in this work have not been previously reported.…”

“…The Genome-Wide Association Study (GWAS) method, combined with novel computational approaches that enhance efficiency 18 , holds significant potential for increasing crop yield by identifying genetic variations linked to desirable traits, thereby enabling more targeted and effective breeding strategies. Recent reports studied the genetic basis and QTLs controlling FL and related morphological traits in wheat using bi-parental populations as well as diverse collections 16 , 17 , 19 – 22 , in addition to other cereals such as barley 23 , 24 and rice 25 , 26 . More precisely, QTLs were underlying FLL such as qFll-4B.1 15 , QFll.sicau-2D.3 and QFll.sicau-5B.3 16 ; FLW like QFlw.sicau-2D 16 , QFlw-4B , QFlw-5B and QFlw-6B 15 , 27 ; FLA such as qFla-4B.1 , qFla-5B , qFla-6B.2 15 , QFla.sicau-2D 16 ; and FLWR like QFlr.sicau-5B 16 and QFlr.cau-5A.2 28 were previously documented in bread wheat.…”

“…For rice, some QTLs for spikelet number per panicle ( Gn1a , Gn1b , and SPP1 ) were reported to be close to qFLL1 , associated with FLL 26 . Promising candidate genes linked with FL morphology traits were previously documented using double haploid (DH), recombinant Inbred Lines (RILs), or F2 populations 15 , 21 , 22 , 30 . For instance, TaFLW1 related to FLW was mapped on 5AL closely related to Fusarium head blight (FHB) resistance gene Fhb5 31 .…”

QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments

“…With the availability of molecular markers and genetic maps, numerous quantitative trait loci (QTLs) related to flag leaf-related traits have been discovered in rice, barley and wheat [ 19 – 22 ]. In rice, Chen et al reported a flag width QTL, qFLW4 , which contains a narrow NAL1 gene with a 74.8 kb interval [ 23 ].…”