Inheritance of the number and thickness of cell layers in barley aleurone tissue (Hordeum vulgare L.): an approach using F2-F3 progeny

Mapping and validation of quantitative trait loci associated with dorsal aleurone thickness in rice (Oryza sativa)

KEY MESSAGE

Mapping of QTLs for dorsal aleurone thickness (DAT) was performed using chromosome segment substitution lines in rice. Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple environments. As a specified endosperm cell type, the aleurone has an abundance of various nutrients. Increasing the number of aleurone layers is a practicable way of developing highly nutritious cereals. Identifying genes that can increase aleurone thickness is useful for the breeding of aleurone traits to improve the nutritional and health values of rice. Here, we found that iodine staining could efficiently distinguish the aleurone layers, which revealed great variation of the aleurone thickness in rice, especially at the dorsal side of the seed. Therefore, we used a population of chromosome segmental substitution lines (CSSLs) derived from Koshihikari and Nona Bokra for quantitative trait locus (QTL) analysis of the dorsal aleurone thickness (DAT). Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple seasons. Among these, qDAT3.2 colocalizes with Hd6 and Hd16, two QTLs previously identified to regulate the heading date of Koshihikari, explaining the negative correlation between the DAT and days to heading (DTH) in rice. We also provide evidence that early-heading ensures the filling of rice seed under a relatively high temperature to promote aleurone thickening. qDAT7.1, the most stable QTL expressed in different environments, functions independently from heading date. Although Nona Bokra has a lower DAT, its qDAT7.1 allele significantly increased DAT in rice, which was further validated using two near-isogenic lines (NILs). These findings pave the way for further gene cloning of aleurone-related QTLs and may aid the development of highly nutritious rice.

Unique Glutelin Expression Patterns and Seed Endosperm Structure Facilitate Glutelin Accumulation in Polyploid Rice Seed

BACKGROUND

Rice is not only an essential food but also a source of high quality protein. Polyploidy is an evolutionary trajectory in plants, and enhancing glutelin by polyploidization is an attractive strategy for improving the nutritional value of rice seeds and presents a great potential for enhancing the commercial value of rice. Elucidating the mechanisms underlying glutelin synthesis and accumulation in tetraploid rice is of great significance.

RESULTS

To enhance the nutritional value of rice, we developed tetraploid rice and evaluated the contents of various nutrient elements in mature seeds. The results revealed a significant increase in protein contents, including the total seed storage proteins, glutelins, and amino acids in tetraploid rice when compared with those in diploid rice. Tandem mass tag-based quantitative proteomic analyses of seeds revealed that glutelins regulated by several glutelin genes in 9311-4x were significantly up-regulated (≥1.5-fold), which was further verified by immunoblot analyses. In addition, temporal expression patterns of various glutelin subunits in different rice lines were investigated. The results revealed significant differences in the expression patterns between diploid and tetraploid rice seeds. Cytohistological analyses results revealed that the thickness of aleurone cell layers increased significantly by 32% in tetraploid rice, the structures of protein storage vacuoles (PSVs) in sub-aleurone cells were more diverse and abundant than those of diploid rice. Temporal expression and proteomic analyses results revealed that protein disulfide isomerase-like 1-1 expression levels were higher in tetraploid rice than in diploid rice, and that the gene responded to oxidative folding with increased levels of proglutelin and appropriate distribution of seed glutelins in tetraploid rice.

CONCLUSION

The results of the present study revealed that polyploidization increased glutelin content by influencing glutelin biosynthesis, transport, and deposition, while variations in glutelin accumulation between tetraploid and diploid rice were largely manifested in the initial time, duration, and relative levels of various glutelin gene expressions during seed filling stages. These findings provide novel insights into improving the protein quality and nutritional value of rice seeds by polyploid breeding.

Molecular Control of Oil Metabolism in the Endosperm of Seeds

In angiosperm seeds, the endosperm develops to varying degrees and accumulates different types of storage compounds remobilized by the seedling during early post-germinative growth. Whereas the molecular mechanisms controlling the metabolism of starch and seed-storage proteins in the endosperm of cereal grains are relatively well characterized, the regulation of oil metabolism in the endosperm of developing and germinating oilseeds has received particular attention only more recently, thanks to the emergence and continuous improvement of analytical techniques allowing the evaluation, within a spatial context, of gene activity on one side, and lipid metabolism on the other side. These studies represent a fundamental step toward the elucidation of the molecular mechanisms governing oil metabolism in this particular tissue. In particular, they highlight the importance of endosperm-specific transcriptional controls for determining original oil compositions usually observed in this tissue. In the light of this research, the biological functions of oils stored in the endosperm of seeds then appear to be more diverse than simply constituting a source of carbon made available for the germinating seedling.

Mutations in the DNA demethylase OsROS1 result in a thickened aleurone and improved nutritional value in rice grains

The rice endosperm, consisting of an outer single-cell layer aleurone and an inner starchy endosperm, is an important staple food for humans. While starchy endosperm stores mainly starch, the aleurone is rich in an array of proteins, vitamins, and minerals. To improve the nutritional value of rice, we screened for mutants with thickened aleurones using a half-seed assay and identified thick aleurone 2-1 (ta2-1), in which the aleurone has 4.8 ± 2.2 cell layers on average. Except for starch, the contents of all measured nutritional factors, including lipids, proteins, vitamins, minerals, and dietary fibers, were increased in ta2-1 grains. Map-based cloning showed that TA2 encodes the DNA demethylase OsROS1. A point mutation in the 14th intron of OsROS1 led to alternative splicing that generated an extra transcript, mOsROS1, with a 21-nt insertion from the intron. Genetic analyses showed that the ta2-1 phenotype is inherited with an unusual gametophytic maternal effect, which is caused not by imprinted gene expression but rather by the presence of the mOsROS1 transcript. Five additional ta2 alleles with the increased aleurone cell layer and different inheritance patterns were identified by TILLING. Genome-wide bisulfite sequencing revealed general increases in CG and CHG methylations in ta2-1 endosperms, along with hypermethylation and reduced expression in two putative aleurone differentiation-related transcription factors. This study thus suggests that OsROS1-mediated DNA demethylation restricts the number of aleurone cell layers in rice and provides a way to improve the nutrition of rice.

Differences in hydrolytic enzyme activity accompany natural variation in mature aleurone morphology in barley (Hordeum vulgare L.)

The aleurone is a critical component of the cereal seed and is located at the periphery of the starchy endosperm. During germination, the aleurone is responsible for releasing hydrolytic enzymes that degrade cell wall polysaccharides and starch granules, which is a key requirement for barley malt production. Inter- and intra-species differences in aleurone layer number have been identified in the cereals but the significance of this variation during seed development and germination remains unclear. In this study, natural variation in mature aleurone features was examined in a panel of 33 Hordeum vulgare (barley) genotypes. Differences were identified in the number of aleurone cell layers, the transverse thickness of the aleurone and the proportion of aleurone relative to starchy endosperm. In addition, variation was identified in the activity of hydrolytic enzymes that are associated with germination. Notably, activity of the free fraction of β-amylase (BMY), but not the bound fraction, was increased at grain maturity in barley varieties possessing more aleurone. Laser capture microdissection (LCM) and transcriptional profiling confirmed that HvBMY1 is the most abundant BMY gene in developing grain and accumulates in the aleurone during early stages of grain fill. The results reveal a link between molecular pathways influencing early aleurone development and increased levels of free β-amylase enzyme, potentially highlighting the aleurone as a repository of free β-amylase at grain maturity.

Differences in hydrolytic enzyme activity accompany natural variation in mature aleurone morphology in barley (Hordeum vulgare L.)

The aleurone is a critical component of the cereal seed and is located at the periphery of the starchy endosperm. During germination, the aleurone is responsible for releasing hydrolytic enzymes that degrade cell wall polysaccharides and starch granules, which is a key requirement for barley malt production. Inter- and intra-species differences in aleurone layer number have been identified in the cereals but the significance of this variation during seed development and germination remains unclear. In this study, natural variation in mature aleurone features was examined in a panel of 33 Hordeum vulgare (barley) genotypes. Differences were identified in the number of aleurone cell layers, the transverse thickness of the aleurone and the proportion of aleurone relative to starchy endosperm. In addition, variation was identified in the activity of hydrolytic enzymes that are associated with germination. Notably, activity of the free fraction of β-amylase (BMY), but not the bound fraction, was increased at grain maturity in barley varieties possessing more aleurone. Laser capture microdissection (LCM) and transcriptional profiling confirmed that HvBMY1 is the most abundant BMY gene in developing grain and accumulates in the aleurone during early stages of grain fill. The results reveal a link between molecular pathways influencing early aleurone development and increased levels of free β-amylase enzyme, potentially highlighting the aleurone as a repository of free β-amylase at grain maturity.

Genetic diversity and trait genomic prediction in a pea diversity panel

BACKGROUND

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection.

RESULTS

A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted.

CONCLUSION

The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.

The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation

The aleurone is the outermost layer of cereal endosperm and functions to digest storage products accumulated in starchy endosperm cells as well as to confer important dietary health benefits. Whereas normal maize (Zea mays [Zm]) has a single aleurone layer, naked endosperm (nkd) mutants produce multiple outer cell layers of partially differentiated cells that show sporadic expression of aleurone identity markers such as a viviparous1 promoter-β-glucuronidase transgene. The 15:1 F2 segregation ratio suggested that two recessive genes were involved, and map-based cloning identified two homologous genes in duplicated regions of the genome. The nkd1 and nkd2 genes encode the INDETERMINATE1 domain (IDD) containing transcription factors ZmIDDveg9 and ZmIDD9 on chromosomes 2 and 10, respectively. Independent mutant alleles of nkd1 and nkd2, as well as nkd2-RNA interference lines in which both nkd genes were knocked down, also showed the nkd mutant phenotype, confirming the gene identities. In wild-type kernels, the nkd transcripts were most abundant around 11 to 16 d after pollination. The NKD proteins have putative nuclear localization signals, and green fluorescent protein fusion proteins showed nuclear localization. The mutant phenotype and gene identities suggest that NKD controls a gene regulatory network involved in aleurone cell fate specification and cell differentiation.

The thick aleurone1 mutant defines a negative regulation of maize aleurone cell fate that functions downstream of defective kernel1

The maize (Zea mays) aleurone layer occupies the single outermost layer of the endosperm. The defective kernel1 (dek1) gene is a central regulator required for aleurone cell fate specification. dek1 mutants have pleiotropic phenotypes including lack of aleurone cells, aborted embryos, carotenoid deficiency, and a soft, floury endosperm deficient in zeins. Here we describe the thick aleurone1 (thk1) mutant that defines a novel negative function in the regulation of aleurone differentiation. Mutants possess multiple layers of aleurone cells as well as aborted embryos. Clonal sectors of thk1 mutant tissue in otherwise normal endosperm showed localized expression of the phenotype with sharp boundaries, indicating a localized cellular function for the gene. Sectors in leaves showed expanded epidermal cell morphology but the mutant epidermis generally remained in a single cell layer. Double mutant analysis indicated that the thk1 mutant is epistatic to dek1 for several aspects of the pleiotropic dek1 phenotype. dek1 mutant endosperm that was mosaic for thk1 mutant sectors showed localized patches of multilayered aleurone. Localized sectors were surrounded by halos of carotenoid pigments and double mutant kernels had restored zein profiles. In sum, loss of thk1 function restored the ability of dek1 mutant endosperm to accumulate carotenoids and zeins and to differentiate aleurone. Therefore the thk1 mutation defines a negative regulator that functions downstream of dek1 in the signaling system that controls aleurone specification and other aspects of endosperm development. The thk1 mutation was found to be caused by a deletion of approximately 2 megabases.

Regulation of aleurone development in cereal grains

The aleurone layer of cereal grains is important biologically as well as nutritionally and economically. Here, current knowledge on the regulation of aleurone development is reviewed. Recent reports suggest that the control of aleurone development is more complex than earlier models portrayed. Multiple levels of genetic regulation control aleurone cell fate, differentiation, and organization. The hormones auxin and cytokinin can also influence aleurone development. New technical advances promise to facilitate future progress.

High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.)

Over the past few years, considerable progress has been made in high-throughput single nucleotide polymorphism (SNP) genotyping technologies, largely through the investment of the human genetics community. These technologies are well adapted to diploid species. For plant breeding purposes, it is important to determine whether these genotyping methods are adapted to polyploidy, as most major crops are former or recent polyploids. To address this problem, we tested the capacity of the multiplex technology SNPlex with a set of 47 wheat SNPs to genotype DNAs of 1314 lines that were organized in four 384-well plates. These lines represented different taxa of tetra- and hexaploid Triticum species and their wild diploid relatives. We observed 40 markers which gave less than 20% missing data. Different methods, based on either Sanger sequencing or the MassARRAY genotyping technology, were then used to validate the genotypes obtained by SNPlex for 11 markers. The concordance of the genotypes obtained by SNPlex with the results obtained by the different validation methods was 96%, except for one discarded marker. Furthermore, a mapping study on six markers showed the expected genetic positions previously described. To conclude, this study showed that high-throughput genotyping technologies developed for diploid species can be used successfully in polyploids, although there is a need for manual reading. For the first time in wheat species, a core of 39 SNPs is available that can serve as the basis for the development of a complete SNPlex set of 48 markers.