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Key message: We developed and validated 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for 46 genes of important wheat quality, biotic and abiotic stress resistance, grain yield, and adaptation-related traits for marker-assisted selection in wheat breeding. Development of high-throughput, low-cost, gene-specific molecular markers is important for marker-assisted selection in wheat breeding. In this study, we developed 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for wheat quality, tolerance to biotic and abiotic stresses, grain yield, and adaptation-related traits. The STARP assays were validated by (1) comparison of the assays with corresponding diagnostic STS/CAPS markers on 40 diverse wheat cultivars and (2) characterization of allelic effects based on the phenotypic and genotypic data of three segregating populations and 305 diverse wheat accessions from China and 13 other countries. The STARP assays showed the advantages of high-throughput, accuracy, flexibility, simple assay design, low operational costs, and platform compatibility. The state-of-the-art assays of this study provide a robust and reliable molecular marker toolkit for wheat breeding programs. [ABSTRACT FROM AUTHOR]

The primary cause of time‐dependent discoloration in wheat (Triticum aestivum L.)‐based products is polyphenol oxidase (PPO) activity. A comprehensive genetic characterization of PPO activity in wheat could expedite the development of wheat varieties with low PPO activity. To dissect the genetic architecture of PPO activity in wheat flour, a panel of 166 diverse bread wheat cultivars was phenotyped in four different environments and genotyped by high‐density wheat 90K and 660K arrays. A genome‐wide association study (GWAS) was performed by a mixed linear model that incorporated population structure and relative kinship. Four hundred and sixty‐five stable marker–trait associations representative of 43 quantitative trait loci (QTL) for PPO activity identified in at least two environments were located on all wheat chromosomes except 5A, with each explaining 6.6–32.4% of the phenotypic variance. Based on IWGSC RefSeq v1.0, we found that QPPO2A.3, QPPO2B.1, QPPO2B.2, and QPPO2D.2 were consistent with the previously reported QTL, and 12 QTL located on homoeologous group 1 chromosomes (6 QTL), chromosomes 4B, 4D, and 7A (2 QTL), and chromosome 7B (2 QTL) are likely to be new PPO loci. Based on physical positions of QTL and previous studies, Ppo‐A1, Ppo‐A2, Ppo‐B2, Ppo‐D2, Pinb‐D1, and genes encoding a Cu ion‐binding protein and a Cu‐transporting ATPase RAN1‐like protein were considered as candidates for QPPO2A.3, QPPO2B.1, QPPO2D.2, QPPO5D.1, QPPO4A.2, and QPPO7D.2, respectively. This study provided insights into the molecular basis of wheat PPO activity, and associated markers can be used for selection of low PPO breeding lines as a means of improving the marketing quality of wheat products. [ABSTRACT FROM AUTHOR]

Key message: Genetic dissection uncovered a major QTL QTKW.caas-4BS corresponding with a 483 kb deletion that included genes ZnF, EamA and Rht-B1. This deletion was associated with increased grain weight and semi-dwarf phenotype. Previous studies identified quantitative trait loci (QTL) for thousand kernel weight (TKW) in the region spanning the Rht-B1 locus in wheat (Triticum aestivum L.). We recently mapped a major QTL QTKW.caas-4BS for TKW spanning the Rht-B1 locus in a recombinant inbred line (RIL) population derived from Doumai/Shi 4185 using the wheat 90K array. The allele from Doumai at QTKW.caas-4BS significantly increased TKW and kernel number per spike, and conferred semi-dwarf trait, which was beneficial to improve grain yield without a penalty to lodging. To further dissect QTKW.caas-4BS, we firstly re-investigated the genotypes and phenotypes of the RILs and confirmed the QTL using cleaved amplified polymorphic sequence (CAPS) markers developed from flanking SNP markers IWA102 and IWB54814. The target sequences of the CAPS markers were used as queries to BLAST the wheat reference genome RefSeq v1.0 and hit an approximate 10.4 Mb genomic region. Based on genomic mining and SNP loci from the wheat 660K SNP array in the above genomic region, we developed eight new markers and narrowed QTKW.caas-4BS to a genetic interval of 1.5 cM. A 483 kb deletion in Doumai corresponded with QTKW.caas-4BS genetically, including three genes ZnF, EamA and Rht-B1. The other 15 genes with either differential expressions and/or sequence variations between parents were also potential candidate genes for QTKW.caas-4BS. The findings not only provide a toolkit for marker-assisted selection of QTKW.caas-4BS but also defined candidate genes for further functional analysis. [ABSTRACT FROM AUTHOR]

Key message: Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued. [ABSTRACT FROM AUTHOR]

Trehalose 6-phosphate phosphatase ( TPP) dephosphorylates trehalose 6-phosphate to trehalose, an important growth regulator, and is involved in starch accumulation and grain yield. In this study, wheat TPP homologs were isolated from chromosomes 6AL, 6BL, and 6DL, designated as TaTPP- 6AL1, TaTPP- 6BL1, and TaTPP-6DL1, respectively. Sequence alignment showed a single-nucleotide polymorphism (SNP) at TaTPP- 6AL1 locus between cultivars with contrasting thousand grain weight (TGW), forming alleles TaTPP- 6AL1a and TaTPP- 6AL1b, respectively. A cleaved amplified polymorphic sequence (CAPS) marker, TaTPP- 6AL1-CAPS, was developed to differentiate the two alleles. TaTPP- 6AL1 was mapped within the interval of IWB65749 and IWB60449 in a recombinant inbred line (RIL) population derived from Zhou8425B/Chinese Spring using the wheat 90K SNP assay. A QTL for TGW identified in the interval explained 12.1 -19.1% of the phenotypic variance across five environments. Association analysis on 141 Chinese wheat cultivars also indicated a significant correlation of TaTPP- 6AL1 with TGW. In conclusion, TaTPP- 6AL1 and its functional marker are valuable to improve grain yield in wheat breeding. [ABSTRACT FROM AUTHOR]

Key message : Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Abstract: Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas- 2AL, QBp.caas- 2BL, QBp.caas- 3AL, QBp.caas- 3BL, QBp.caas- 5AS, QBp.caas- 6A, QBp.caas- 7AL.1, QBp.caas- 7AL.2 and QBp.caas- 7BS, respectively. All resistance alleles, except for QBp.caas- 7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas- 3BL, QBp.caas- 5AS, QBp.caas- 7AL.1, QBp.caas- 7AL.2 and QBp.caas- 7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance. [ABSTRACT FROM AUTHOR]

Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs) distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs), and 11 MTAs were identified in two or more environments. Liner regression showed a clear dependence of WSC BLUE scores on numbers of favorable (increasing WSC content) and unfavorable alleles (decreasing WSC), indicating that genotypes with higher numbers of favorable or lower numbers of unfavorable alleles had higher WSC content. In silico analysis of flanking sequences of trait-associated SNPs revealed eight candidate genes related to WSC content grouped into two categories based on the type of encoding proteins, namely, defense response proteins and proteins triggered by environmental stresses. The identified SNPs and candidate genes related to WSC provide opportunities for breeding higher WSC wheat cultivars. [ABSTRACT FROM AUTHOR]