Physical mapping and a new variant of Puroindoline b-2 genes in wheat

Quality traits analysis of 153 wheat lines derived from CIMMYT and China

In order to understand the difference of quality for Chinese and CIMMYT wheat varieties (lines), we selected 153 wheat germplasm from both China and CIMMYT to explore the contribution relationship of different allelic variation combinations to wheat quality through genotyping and phenotyping, including grain hardness, polyphenol oxidase (PPO) activity, lipoxygenase (LOX) activity, yellow pigment (YP) content and protein content. In terms of flour milling quality, Chinese wheat varieties were mainly carrying Pina-D1a/Pinb-D1b, accounting for 32.0% of the total tested varieties, while the CIMMYT wheat lines were mainly carrying Pina-D1b/Pinb-D1a with 45.8% of the total collection. The distribution frequencies of subunit 1/2* and 5 + 10 were 47.0% and 42.5%, respectively, in CIMMYT varieties, however they were only 31.4% and 13.7% respectively of the Chinese wheat tested varieties. In addition, the proportion of phytoene synthase (PSY) allele, PPO allele and LOX active allele were roughly the same between Chinese and CIMMYT varieties. Based on the present study, we found that Pina gene had a greater impact on grain hardness value than Pinb gene; The influence of PPO-A1 gene on polyphenol oxidase activity was more significant than PPO-D1 gene. The high protein content of varieties mostly containing hardness genes and 1/2*/5 + 10 subunit combinations. Based on the present study, we found that the quality gene distribution of Chinese and CIMMYT varieties was quite different, for instance, the high-quality HMW-GS subunits of Chinese varieties were lower than CIMMYT lines. It will be much useful for Chinese wheat breeders to develop good quality wheat variety by crossing with 3 good strong gluten CIMMYT wheat lines by molecular marker-assisted selection.

Understanding Wheat Starch Metabolism in Properties, Environmental Stress Condition, and Molecular Approaches for Value-Added Utilization

Wheat starch is one of the most important components in wheat grain and is extensively used as the main source in bread, noodles, and cookies. The wheat endosperm is composed of about 70% starch, so differences in the quality and quantity of starch affect the flour processing characteristics. Investigations on starch composition, structure, morphology, molecular markers, and transformations are providing new and efficient techniques that can improve the quality of bread wheat. Additionally, wheat starch composition and quality are varied due to genetics and environmental factors. Starch is more sensitive to heat and drought stress compared to storage proteins. These stresses also have a great influence on the grain filling period and anthesis, and, consequently, a negative effect on starch synthesis. Sucrose metabolizing and starch synthesis enzymes are suppressed under heat and drought stress during the grain filling period. Therefore, it is important to illustrate starch and sucrose mechanisms during plant responses in the grain filling period. In recent years, most of these quality traits have been investigated through genetic modification studies. This is an attractive approach to improve functional properties in wheat starch. The new information collected from hybrid and transgenic plants is expected to help develop novel starch for understanding wheat starch biosynthesis and commercial use. Wheat transformation research using plant genetic engineering technology is the main purpose of continuously controlling and analyzing the properties of wheat starch. The aim of this paper is to review the structure, biosynthesis mechanism, quality, and response to heat and drought stress of wheat starch. Additionally, molecular markers and transformation studies are reviewed to elucidate starch quality in wheat.

Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species

Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci Pinb2 not syntenic to the Hardness locus, with Pinb2-7A locus containing three tandem copies. PINB2 proteins have several features conserved for the Pin/Pinb2 phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. Pinb2 are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new Pinb2 allele specific markers and demonstrated their usefulness by 1) identifying new Pinb2 alleles in Triticeae species; and 2) performing an association analysis of Pinb2 with kernel hardness. The association result suggests that Pinb2 genes may have no substantial contribution to kernel hardness. Our results provide new insights into Pinb2 evolution and expression and the new allele-specific markers are useful to further explore Pinb2's contribution to seed traits in wheat.

Evaluation of the genetic architecture and the potential of genomics-assisted breeding of quality traits in two large panels of durum wheat

New QTL for important quality traits in durum were identified, but for most QTL their effect varies depending on the investigated germplasm. Most of the global durum wheat (Triticum turgidum ssp. durum) production is used for human consumption via pasta and to a lower extent couscous and bulgur. Therefore, durum wheat varieties have to fulfill high demands regarding quality traits. In this study, we evaluated the quality traits protein content, sedimentation volume, falling number, vitreousity and thousand kernel weight in a Central European (CP) and a Southern and Western European panel (SP) with 183 and 159 durum lines, respectively, and investigated their genetic architecture by genome-wide association mapping. Except for protein content, we identified QTL explaining a large proportion of the genotypic variance for different traits. However, most of them were identified only in one panel. Nevertheless, for sedimentation volume a genomic region on chromosome 1B appeared important in both durum panels and a BLAST search against the emmer and bread wheat reference genomes points toward the candidate gene Glu-B3. This was further supported by the protein subunit banding pattern via SDS-PAGE gel electrophoresis. For vitreousity, genomic regions on chromosome 7A explained a larger proportion of the genotypic variance in both panels, whereas one QTL, possibly related to the Pinb-2 locus, also slightly influenced the protein content. Within each panel, high prediction abilities for genomic selection were obtained, which, however, dropped considerably when predicting across both panels. Nevertheless, the across-panel prediction ability was still larger than 0.4 for protein content and sedimentation volume, underlining the potential for genomics-aided durum breeding, if laboratory and logistical facilities are available.

Sequence Diversity and Identification of Novel Puroindoline and Grain Softness Protein Alleles in Elymus, Agropyron and Related Species

The puroindoline proteins, PINA and PINB, which are encoded by the Pina and Pinb genes located at the Ha locus on chromosome 5D of bread wheat, are considered to be the most important determinants of grain hardness. However, the recent identification of Pinb-2 genes on group 7 chromosomes has stressed the importance of considering the effects of related genes and proteins. Several species related to wheat (two diploid Agropyron spp., four tetraploid Elymus spp. and five hexaploid Elymus and Agropyron spp.) were therefore analyzed to identify novel variation in Pina, Pinb and Pinb-2 genes which could be exploited for the improvement of cultivated wheat. A novel sequence for the Pina gene was detected in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus and Elymus nutans and novel PINB sequences in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus, and Elymus nutans. A novel PINB-2 variant was also detected in Agropyron repens and Elymus repens. The encoded proteins detected all showed changes in the tryptophan-rich domain as well as changes in and/or deletions of basic and hydrophobic residues. In addition, two new AGP sequences were identified in Elymus nutans and Elymus wawawaiensis. The data presented therefore highlight the sequence diversity in this important gene family and the potential to exploit this diversity to modify grain texture and end-use quality in wheat.

Influence of Gene Expression on Hardness in Wheat

Puroindoline (Pina and Pinb) genes control grain texture or hardness in wheat. Wild-type/soft alleles lead to softer grain while a mutation in one or both of these genes results in a hard grain. Variation in hardness in genotypes with identical Pin alleles (wild-type or mutant) is known but the molecular basis of this is not known. We now report the identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes. RNA-Seq analysis was used to determine the variation in the transcriptome of developing grains of thirty three diverse wheat genotypes including hard (mutant Pin) and soft (wild type) and those that were hard without having Pin mutations. This defined the role of pin gene expression and identified other candidate genes associated with hardness. Pina was not expressed in hard wheat with a mutation in the Pina gene. The ratio of Pina to Pinb expression was generally lower in the hard non mutant genotypes. Hardness may be associated with differences in Pin expression and other factors and is not simply associated with mutations in the PIN protein coding sequences.

Development and validation of KASP assays for genes underpinning key economic traits in bread wheat

We developed and validated a robust marker toolkit for high-throughput and cost-effective screening of a large number of functional genes in wheat. Functional markers (FMs) are the most valuable markers for crop breeding programs, and high-throughput genotyping for FMs could provide an excellent opportunity to effectively practice marker-assisted selection while breeding cultivars. Here we developed and validated kompetitive allele-specific PCR (KASP) assays for genes that underpin economically important traits in bread wheat including adaptability, grain yield, quality, and biotic and abiotic stress resistances. In total, 70 KASP assays either developed in this study or obtained from public databases were validated for reliability in application. The validation of KASP assays were conducted by (a) comparing the assays with available gel-based PCR markers on 23 diverse wheat accessions, (b) validation of the derived allelic information using phenotypes of a panel comprised of 300 diverse cultivars from China and 13 other countries, and (c) additional testing, where possible, of the assays in four segregating populations. All KASP assays being reported were significantly associated with the relevant phenotypes in the cultivars panel and bi-parental populations, thus revealing potential application in wheat breeding programs. The results revealed 45 times superiority of the KASP assays in speed than gel-based PCR markers. KASP has recently emerged as single-plex high-throughput genotyping technology; this is the first report on high-throughput screening of a large number of functional genes in a major crop. Such assays could greatly accelerate the characterization of crossing parents and advanced lines for marker-assisted selection and can complement the inflexible, high-density SNP arrays. Our results offer a robust and reliable molecular marker toolkit that can contribute towards maximizing genetic gains in wheat breeding programs.

Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat.

Genetic control of grain yield and grain physical characteristics in a bread wheat population grown under a range of environmental conditions

Genetic analysis of the yield and physical quality of wheat revealed complex genetic control, including strong effects of photoperiod-sensitivity loci. Environmental conditions such as moisture deficit and high temperatures during the growing period affect the grain yield and grain characteristics of bread wheat (Triticum aestivum L.). The aim of this study was to map quantitative trait loci (QTL) for grain yield and grain quality traits using a Drysdale/Gladius bread wheat mapping population grown under a range of environmental conditions in Australia and Mexico. In general, yield and grain quality were reduced in environments exposed to drought and/or heat stress. Despite large effects of known photoperiod-sensitivity loci (Ppd-B1 and Ppd-D1) on crop development, grain yield and grain quality traits, it was possible to detect QTL elsewhere in the genome. Some of these QTL were detected consistently across environments. A locus on chromosome 6A (TaGW2) that is known to be associated with grain development was associated with grain width, thickness and roundness. The grain hardness (Ha) locus on chromosome 5D was associated with particle size index and flour extraction and a region on chromosome 3B was associated with grain width, thickness, thousand grain weight and yield. The genetic control of grain length appeared to be largely independent of the genetic control of the other grain dimensions. As expected, effects on grain yield were detected at loci that also affected yield components. Some QTL displayed QTL-by-environment interactions, with some having effects only in environments subject to water limitation and/or heat stress.

A review of the occurrence of Grain softness protein-1 genes in wheat (Triticum aestivum L.)

Grain softness protein-1 (Gsp-1) is a small, 495-bp intronless gene found throughout the Triticeae tribe at the distal end of group 5 chromosomes. With the Puroindolines, it constitutes a key component of the Hardness locus. Gsp-1 likely plays little role in grain hardness, but has direct interest due to its utility in phylogeny and its role in arabinogalactan peptides. Further role(s) remain to be identified. In the polyploid wheats, Triticum aestivum and T. turgidum, the gene is present in a homoeologous series. Since its discovery, there have been conflicting reports and data as to the number of Gsp-1 genes and the level of sequence polymorphism. Little is known about allelic variation within a species. In the simplest model, a single Gsp-1 gene is present in each wheat and Aegilops tauschii genome. The present review critically re-examines the published and some unpublished data (sequence available in the NCBI nucleotide and MIPS Wheat Genome Databases). A number of testable hypotheses are identified, and include the level of polymorphism that may represent (and define) different Gsp-1 alleles, the existence of a fourth Gsp-1 gene, and the apparent, at times, high level of naturally-occurring or artifactual gene chimeras. In summary, the present data provide firm evidence for at most, three Gsp-1 genes in wheat, although there are numerous data that suggest a more complex model.

Sina and Sinb genes in triticale do not determine grain hardness contrary to their orthologs Pina and Pinb in wheat

BACKGROUND

Secaloindoline a (Sina) and secaloindoline b (Sinb) genes of hexaploid triticale (x Triticosecale Wittmack) are orthologs of puroindoline a (Pina) and puroindoline b (Pinb) in hexaploid wheat (Triticum aestivum L.). It has already been proven that RNA interference (RNAi)-based silencing of Pina and Pinb genes significantly decreased the puroindoline a and puroindoline b proteins in wheat and essentially increased grain hardness (J Exp Bot 62:4025-4036, 2011). The function of Sina and Sinb in triticale was tested by means of RNAi silencing and compared to wheat.

RESULTS

Novel Sina and Sinb alleles in wild-type plants of cv. Wanad were identified and their expression profiles characterized. Alignment with wheat Pina-D1a and Pinb-D1a alleles showed 95% and 93.3% homology with Sina and Sinb coding sequences. Twenty transgenic lines transformed with two hpRNA silencing cassettes directed to silence Sina or Sinb were obtained by the Agrobacterium-mediated method. A significant decrease of expression of both Sin genes in segregating progeny of tested T1 lines was observed independent of the silencing cassette used. The silencing was transmitted to the T4 kernel generation. The relative transcript level was reduced by up to 99% in T3 progeny with the mean for the sublines being around 90%. Silencing of the Sin genes resulted in a substantial decrease of secaloindoline a and secaloindoline b content. The identity of SIN peptides was confirmed by mass spectrometry. The hardness index, measured by the SKCS (Single Kernel Characterization System) method, ranged from 22 to 56 in silent lines and from 37 to 49 in the control, and the mean values were insignificantly lower in the silent ones, proving increased softness. Additionally, the mean total seed protein content of silenced lines was about 6% lower compared with control lines. Correlation coefficients between hardness and transcript level were weakly positive.

CONCLUSIONS

We documented that RNAi-based silencing of Sin genes resulted in significant decrease of their transcripts and the level of both secaloindoline proteins, however did not affect grain hardness. The unexpected, functional differences of Sin genes from triticale compared with their orthologs, Pin of wheat, are discussed.

Identification and distribution of Puroindoline b-2 variant gene homologs in Hordeum

The barley hordoindoline genes (Hina and Hinb) are homologous to the wheat puroindoline genes (Pina and Pinb). These genes are involved in grain hardness, which is an important quality for barley processing. We identified novel variants of Hina and Hinb in 10 wild Hordeum species (H. bogdanii, H. brachyantherum, H. bulbosum, H. chilense, H. comosum, H. marinum, H. murinum, H. patagonicum, H. pusillum, and H. roshevitzii) covering all Hordeum genomes and preliminarily named them Hinc. These nucleotide sequences were highly similar to those of Puroindoline b-2 variant genes (Pinb-2v) and were located on chromosome 7I in H. chilense. The Hinc genes in H. bogdanii, H. bulbosum, H. patagonicum, and H. roshevitzii were pseudogenes possessing in-frame stop codons. We also found a partial Hinc sequence in H. murinum. This gene was not found in cultivated barley and H. vulgare subsp. spontaneum. The phylogenetic tree of Gsp-1, Hin, and Pin genes demonstrates that Hinc and Pinb-2v genes formed one cluster. Therefore, we considered that Hinc and Pinb-2v genes shared a common ancestral gene and were homologous to each other. We also studied the evolutional process of Gsp-1, Hin, and Pin genes. Our results suggested that Gsp-1 might be the most closely related to a putative ancestral gene on Ha locus.

Discovery, distribution and diversity of Puroindoline-D1 genes in bread wheat from five countries (Triticum aestivum L.)

BACKGROUND

Grain texture is one of the most important characteristics in bread wheat (Triticum aestivum L.). Puroindoline-D1 genes play the main role in controlling grain texture and are intimately associated with the milling and processing qualities in bread wheat.

RESULTS

A series of diagnostic molecular markers and dCAPS markers were used to characterize Pina-D1 and Pinb-D1 in 493 wheat cultivars from diverse geographic locations. A primer walking strategy was used to characterize PINA-null alleles at the DNA level. Results indicated that Chinese landraces encompassing 12 different Puroindoline-D1 allelic combinations showed the highest diversity, while CIMMYT wheat cultivars containing 3 different Puroindoline-D1 allelic combinations showed the lowest diversity amongst wheat cultivars from the five countries surveyed. Two novel Pina-D1 alleles, designated Pina-D1s with a 4,422-bp deletion and Pina-D1u with a 6,460-bp deletion in the Ha (Hardness) locus, were characterized at the DNA level by a primer walking strategy, and corresponding molecular markers Pina-N3 and Pina-N4 were developed for straightforward identification of the Pina-D1s and Pina-D1u alleles. Analysis of the association of Puroindoline-D1 alleles with grain texture indicated that wheat cultivars with Pina-null/Pinb-null allele, possessing an approximate 33-kb deletion in the Ha locus, have the highest SKCS hardness index amongst the different genotypes used in this study. Moreover, wheat cultivars with the PINA-null allele have significantly higher SKCS hardness index than those of Pinb-D1b and Pinb-D1p alleles.

CONCLUSIONS

Molecular characterization of the Puroindoline-D1 allele was investigated in bread wheat cultivars from five geographic regions, resulting in the discovery of two new alleles - Pina-D1s and Pina-D1u. Molecular markers were developed for both alleles. Analysis of the association of the Puroindoline-D1 alleles with grain texture showed that cultivars with PINA-null allele possessed relatively high SKCS hardness index. This study can provide useful information for the improvement of wheat quality, as well as give a deeper understanding of the molecular and genetic processes controlling grain texture in bread wheat.

Prevalence of Puroindoline D1 and Puroindoline b-2 variants in U.S. Pacific Northwest wheat breeding germplasm pools, and their association with kernel texture

Kernel texture is a major factor influencing the classification and end use properties of wheat (Triticum aestivum L.), and is mainly controlled by the Puroindoline a (Pina) and Puroindoline b (Pinb) genes. Recently, a new puroindoline gene, Puroindoline b-2 (Pin b-2), was identified. In this study, 388 wheat cultivars and advanced breeding lines from the U.S. Pacific Northwest were investigated for frequencies of Puroindoline D1 alleles and Pinb-2 variants 2 and 3. Results indicated that Pinb-D1b (74.0%) was the predominant genotype among hard wheats (N = 196), the only other hard allele encountered was Pina-D1b (26.0%). Across all varieties, Pinb-2v3 was the predominant genotype (84.5%) compared with Pinb-2v2 (15.5%). However, among 240 winter wheat varieties (124 soft white, 15 club, 68 hard red and 33 hard white varieties), all carried Pinb-2v3. Among spring wheats, Pinb-2v2 and Pinb-2v3 frequencies were more variable (soft white 25.0:75.0, hard red 58.2:41.8 and hard white 40.0:60.0, respectively). Kernel texture variation was analyzed using 247 of the 388 wheat varieties grown in multi-location factorial trials in up to 7 crop years. The range of variety means among the four groups, soft winter, soft spring, hard winter and hard spring, was on the order of 15-25 single kernel characterization system (SKCS) Hardness Index. The least significant difference for each of these trials ranged from 2.8 to 5.6 SKCS Hardness Index. Observations lead to the conclusion that Pinb-2 variants do not exert a prominent effect on kernel texture, however, Pinb-2 variants do identify features of wheat germ plasm structure in the U.S. Pacific Northwest.