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Eight major and stably expressed QTL for flag leaf morphology across eleven environments were identified and validated using newly developed KASP markers in seven biparental populations with different genetic backgrounds. Flag leaf morphology is a determinant trait influencing plant architecture and yield potential in wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population with a 55 K SNP-based constructed genetic map was used to map quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), area (FLA), angle (FLANG), opening angle (FLOA), and bend angle (FLBA) in eleven environments. Eight major QTL were detected in 11 environments with 5.73–54.38% of explained phenotypic variation. These QTL were successfully verified using the newly developed Kompetitive Allele Specific PCR (KASP) markers in six biparental populations with different genetic backgrounds. Among these 8 major QTL, two co-located intervals were identified. Significant interactions for both FLL- and FLW-related QTL were detected. Comparison analysis showed that QFll.sau-SY-2B and QFla.sau-SY-2B are likely new loci. Significant relationships between flag leaf- and yield-related traits were observed and discussed. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat ‘Chinese spring’, T. turgidum, and Aegilops tauschii. Taken together, these results broaden our understanding on genetic basis of flag leaf morphology and provide clues for fine mapping and marker-assisted breeding wheat with optimized plant architecture for promising loci.

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A major and stably expressed QTL for spikelet number per spike identified in a 2-cM interval on chromosome arm 2DS was validated using two populations with different genetic backgrounds. Spikelet number per spike (SNS) plays a key role in wheat yield improvement. Numerous genetic and environmental factors influencing SNS have been documented, but the number of major, stably expressed and validated loci underlying SNS is still limited. In this study, a recombinant inbred line (RIL) population derived from a normal spikelet cultivar and a multiple-spikelet wheat line (with a longer spike with more canonically oriented apical spikelets) was genotyped using a Wheat55K single-nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers. SNS was measured for this RIL population in eight environments. Five QTL were each identified in two or more environments. One of them, QSns.sau-2D (LOD = 3.47–38.24, PVE = 10.16–45.68%), was detected in all the eight environments. The QTL was located in a 2-cM interval on chromosome arm 2DS flanked by the markers AX-109836946 and AX-111956072. This QTL, QSns.sau-2D, significantly increased SNS by up to 14.72%. Several genes associated with plant growth and development were identified in the physical interval of QSns.sau-2D. This QTL was further validated by the tightly linked Kompetitive Allele Specific PCR (KASP) marker, KASP-AX-94721936, in two other populations with different genetic backgrounds. The significant correlation between SNS and anthesis date, plant height, spike length, grain number per spike and thousand-grain weight were detected and discussed. These results lay the foundation for fine mapping and cloning gene(s) underlying QSns.sau-2D.

An EMS-induced single-base mutation at a splice site caused abnormal RNA splicing and resulted in the gene inactivation and the lack of Wx-A1 protein in a wheat EMS mutant line. An EMS-mutagenized population was generated using common wheat cv. SM126 consisting of 10,600 M2 plants. One Wx-A1 null mutant was identified through analyses of 390 grains produced from 130 M2 plants using electrophoresis analyses. The Wx-A1 sequences of parental line SM126 and M2-31 mutant were determined as 2781 bp, and there was only one SNP mutation between them. The SNP was a mutation from G to A at nucleotide sequence position 2168 bp (G2168A) downstream of the start codon which was located at the splicing site within the eighth intron. All 52 cDNA transcripts were found to be incorrectly spliced and can be summarized as five types of variations. The deletion of the exon and the exclusion of intron were structural features in abnormal splicing RNA. Together with the prediction of potential splice regulatory motifs, the mutation G2168A happened within the 5′ splice site of the eighth intron and destroyed the splice donor site from GU to AU, which may have brought about a barrier against correct RNA splice, and generated abnormal mRNA, which was the mechanism of the inactivation of Wx-A1 in M2-31. The lack of Wx-A1 has resulted in changes in starch properties in the M2-31 mutant, with the reduction in amylose and starch contents. The increased grains hardness was observed in M2-31, which may be related to the lower expression level of Pinb-D1 gene. As the waxy wheat foods have a lot of advantages, the null waxy genes will be widely applied in breeding waxy wheat for varied amylose contents.