Two genes controlling the purple pericarp trait in wheat, TaPpm1 and TaPpb1, are identified and the mechanism by which they co-regulate anthocyanin synthesis is proposed.

The branched spike phenotype is an important supernumerary spikelet trait of Triticum turgidum L. associated with the production of significantly more grains per spike, thereby offering a higher potential yield. However, the genetic basis of branch meristem (BM) development remains to be fully elucidated in wheat. TAW1, an ALOG (Arabidopsis LSH1 and Oryza G1) family gene, has been shown to function as a unique regulator in promoting BM development in rice. In this study, we found that the development pattern of the BMs of the branched spike in wheat was similar to the indeterminate BMs of rice. Moreover, phylogenetic analysis classified the ALOG genes into 12 groups. This family of genes was found to have evolved independently in eudicots and monocots and was evolutionarily conserved between wheat and rice as well as during wheat polyploidization. Furthermore, experiments revealed that TtALOG2-1A, a TAW1-homologous gene, plays a significant role in regulating the transition of indeterminate BM fate. Finally, large-scale RNA-sequencing studies and quantitative real-time polymerase chain reaction (qRT-PCR) experiments revealed that members of the TtALOGs may act upstream of the TtMADS22, TtMADS47, and TtMADS55 genes to promote indeterminate BM activities. Our findings further knowledge on BM development in wheat.

Blue grained wheat contained a higher quantity of natural anthocyanin compounds while normal commercial wheat does not have. Though the genes related to several colours of wheat have been identified, the major genes in blue wheat are still unrevealed. Hence, combining the SNP mapping, and transcriptome analysis, pivotal genes regulating blue grain trait was identified. SNP genotyping was carried out in an F2 blue and white wheat population. The blue trait was controlled by a gene/locus located between two SNP markers of IWB 18525 and IWB16381 on the 4D chromosome. Comparative transcriptome analysis revealed that 40 structural differentially expressed genes (DEGs) related to anthocyanin biosynthesis had significant expression differences between blue and non-blue samples. Among them, 12 DEGs expressed only in blue samples while 2 DEGs were specific to blue wheat. Only two F3'5'H genes located in 4D (Traes_4DL_27C195FDE, Traes_4DL_5A3D8F519) were consistent with the location results performed in SNP genotyping. Further, F3'5'H is considered as the main enzyme for Delphinidin compounds, cause for blue colouration. Hence, two genes encoding F3'5'H in the 4D chromosome preferentially account for the blue pigmentation in wheat.

Fatty acyl-CoA reductase (FAR) is involved in the biosynthesis of 12 primary alcohols, which are waxy constituents that play an important role in 13 plant stress. Previous studies have shown that primary alcohol is the most 14 important component in the wheat seeding stage and accounts for more than 15 80% of the total composition. To date, eight FAR genes have been identified in 16 wheat, but there has not been a systematic analysis. In this study, a 17 comprehensive overview of the TaFAR gene family was performed, including 18 analyses of the phylogenetic relationship, the multiple sequence alignment, the 19 conserved motif distribution and the expression pattern. The result showed 20 that a total of 41 wheat FAR genes were identified and designated TaFAR1-A-21 TaFAR22-D; all FAR genes were divided into six classes according to their 22 phylogenetic relationship, and most of the FAR genes might be related to 23 wheat cuticular wax synthesis. The analysis of the promoter binding site 24 showed that TaFAR genes could be regulated by the MYB transcription factor 25 and could be used as target genes for hormone regulation under adverse 26 conditions, especially during a drought. This study provides a basis for further 27 analyses of the TaFAR gene function and of upstream regulatory genes. 28 29 Keywords: fatty acyl-CoA reductase, cuticular wax, Triticum aestivum 30 31 32 Wheat (Triticum aestivum) is one of the world's most important food crops and 33 feeds one-fifth of the population. Wheat yield is constrained by many factors, 34 including biotic and abiotic stresses [1]. Drought is a major threat to wheat 35 production [2]. The surface of wheat is covered with cuticular wax, which plays 36 important roles in drought tolerance by limiting nonstomatal water loss [3]. 37 Cuticular wax is a complex mixture of lipids and consists of very-long-chain 38 fatty acids (VLCFAs) and their derivatives, including aldehydes, alkanes, 39 alcohols, wax esters and ketones [4-7]. At the wheat seeding stage, primary 40 alcohol is the most important component of cuticular wax and accounts for 41 more than 80% of the total composition. Previous studies demonstrated that 42 primary alcohols were synthesized by fatty acyl-CoA reductase (FAR) [8-13]. In 43 Arabidopsis, the gene family contains eight members, and only the 44 AtFAR3/CER4 gene was involved in the primary alcohols biosynthesis of 45 cuticular wax. However, eight TaFAR genes that are related to the biosynthesis 46 of cuticular wax were identified in wheat, which suggested that there are a 47 series of TaFAR genes involved in wax biosynthesis in wheat. With the gradual 48 improvement of whole-genome sequencing and the annotation of wheat, it was 49 possible to discover its FAR gene family [14]. 50 A typical FAR protein contained an NAD(P)H binding Rossmann-fold (NADB) 51 domain with Pfam ID: PF07993 and a fatty acyl-CoA reductase ('FAR_C') 52 domain with PF03015 [15]. Thus, FARs were predicted to be extended 53 short-chain dehydrogenase/reductase proteins at the N-terminus...