RFLP mapping of the maize dzr1 locus, which regulates methionine-rich 10 kDa zein accumulation

Genetic and molecular understanding for the development of methionine-rich maize: a holistic approach

Maize (Zea mays) is the most important coarse cereal utilized as a major energy source for animal feed and humans. However, maize grains are deficient in methionine, an essential amino acid required for proper growth and development. Synthetic methionine has been used in animal feed, which is costlier and leads to adverse health effects on end-users. Bio-fortification of maize for methionine is, therefore, the most sustainable and environmental friendly approach. The zein proteins are responsible for methionine deposition in the form of δ-zein, which are major seed storage proteins of maize kernel. The present review summarizes various aspects of methionine including its importance and requirement for different subjects, its role in animal growth and performance, regulation of methionine content in maize and its utilization in human food. This review gives insight into improvement strategies including the selection of natural high-methionine mutants, molecular modulation of maize seed storage proteins and target key enzymes for sulphur metabolism and its flux towards the methionine synthesis, expression of synthetic genes, modifying gene codon and promoters employing genetic engineering approaches to enhance its expression. The compiled information on methionine and essential amino acids linked Quantitative Trait Loci in maize and orthologs cereals will give insight into the hotspot-linked genomic regions across the diverse range of maize germplasm through meta-QTL studies. The detailed information about candidate genes will provide the opportunity to target specific regions for gene editing to enhance methionine content in maize. Overall, this review will be helpful for researchers to design appropriate strategies to develop high-methionine maize.

Genetic diversity and evolution of reduced sulfur storage during domestication of maize

The domestication of maize has spanned a period of over 9000 years, during which time its wild relative teosinte underwent natural and artificial selection. We hypothesize that environmental conditions could have played a major role in this process. One factor of environmental variation is soil composition, which includes sulfur availability. Sulfur is reduced during photosynthesis and is used to synthesize cysteine and methionine, which drive the accumulation of δ10 (Zm00001d045937), δ18 (Zm00001d037436), β15 (Zm00001d035760), γ16 (Zm00001d005793), γ27 (Zm00001d020592), and γ50 (Zm00001d020591) zeins, representing the zein2 fraction (z2) of storage proteins in maize seeds. In this study, polymorphisms and haplotypes were detected based on six z2 genes in 60 maize and teosintes lines. Haplotypes were unevenly distributed, and abundant genetic diversity was found in teosintes. Polymorphism was highest in z2δ18, whereas for z2β15 single nucleotide polymorphism (SNP) density and insertion/deletion (indel) abundance were the lowest, indicating differential roles in seed evolution. Indels showed a clustered distribution, and most of these derived from teosintes. The indels not only led to tandem repeat polymorphisms, but also to frameshift mutations, which could also be used as null variants. In addition, neutral evolutionary tests, phylogenetic analyses, and population structures indicated that z2δ10 and z2γ50 had undergone natural selection. Indeed, a natural selection imprint could also be found with z2γ27 and z2γ16, whereas z2δ18 and z2β15 tended to be under neutral evolution. These results suggested that genetic diversity and evolution of a subset of sulfur-rich zeins could be under environmental adaptation during maize domestication.

Genetic and biochemical differences in populations bred for extremes in maize grain methionine concentration

BACKGROUND

Methionine is an important nutrient in animal feed and several approaches have been developed to increase methionine concentration in maize (Zea mays L.) grain. One approach is through traditional breeding using recurrent selection. Using divergent selection, genetically related populations with extreme differences in grain methionine content were produced. In order to better understand the molecular mechanisms controlling grain methionine content, we examined seed proteins, transcript levels of candidate genes, and genotypes of these populations.

RESULTS

Two populations were selected for high or low methionine concentration for eight generations and 40 and 56% differences between the high and low populations in grain methionine concentration were observed. Mean values between the high and low methionine populations differed by greater than 1.5 standard deviations in some cycles of selection. Other amino acids and total protein concentration exhibited much smaller changes. In an effort to understand the molecular mechanisms that contribute to these differences, we compared transcript levels of candidate genes encoding high methionine seed storage proteins involved in sulfur assimilation or methionine biosynthesis. In combination, we also explored the genetic mechanisms at the SNP level through implementation of an association analysis. Significant differences in methionine-rich seed storage protein genes were observed in comparisons of high and low methionine populations, while transcripts of seed storage proteins lacking high levels of methionine were unchanged. Seed storage protein levels were consistent with transcript levels. Two genes involved in sulfur assimilation, Cys2 and CgS1 showed substantial differences in allele frequencies when two selected populations were compared to the starting populations. Major genes identified across cycles of selection by a high-stringency association analysis included dzs18, wx, dzs10, and zp27.

CONCLUSIONS

We hypothesize that transcriptional changes alter sink strength by altering the levels of methionine-rich seed storage proteins. To meet the altered need for sulfur, a cysteine-rich seed storage protein is altered while sulfur assimilation and methionine biosynthesis throughput is changed by selection for certain alleles of Cys2 and CgS1.

Non-Mendelian regulation and allelic variation of methionine-rich delta-zein genes in maize

Sufficient methionine levels in the seed are critical for the supply of a balanced diet for feed and food. Currently, animal feed is supplemented with chemically synthesized methionine, which could be completely replaced with naturally synthesized methionine. However, insufficient levels of methionine are due to alleles of two genes in the maize genome that are expressed during seed development, which have a high percentage of methionine codons, ranging from 23 to 28%, while free methionine is very low. The two genes, dzs10 and dzs18, belong to the prolamin gene family that arose during the evolution of the grasses and were duplicated during a whole genome duplication event. We have found several dzs10 and dzs18 null alleles caused either by transposon insertion or frame shift mutations. Maize seeds with null mutations of both genes have a normal phenotype in contrast to other prolamin genes, explaining the accumulation of methionine deficiency in normal breeding efforts. Moreover, the trans-regulation of these genes deviates from Mendelian inheritance. One allele of the regulatory locus dzr1 is inherited in a parent-of-origin fashion, while another allele appears to prevent Mendelian segregation of the high-methionine phenotype in backcrosses.

Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family

We have isolated and sequenced all 23 members of the 22-kD alpha zein (z1C) gene family of maize. This is one of the largest plant gene families that has been sequenced from a single genetic background and includes the largest contiguous genomic DNA from maize with 346,292 bp to date. Twenty-two of the z1C members are found in a roughly tandem array on chromosome 4S forming a dense gene cluster 168,489-bp long. The twenty-third copy of the gene family is also located on chromosome 4S at a site approximately 20 cM closer to the centromere and appears to be the wild-type allele of the floury-2 (fl2) mutation. On the basis of an analysis of maize cDNA databases, only seven of these genes appear to be expressed including the fl2 allele. The expressed genes in the cluster are interspersed with nonexpressed genes. Interestingly, some of the expressed genes differ in their transcriptional regulation. Gene amplification appears to be in blocks of genes explaining the rapid and compact expansion of the cluster during the evolution of maize.

Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes

The short arm of Triticeae homeologous group 1 chromosomes is known to contain many agronomically important genes. The objectives of this study were to physically localize gene-containing regions of the group 1 short arm, enrich these regions with markers, and study the distribution of genes and recombination. We focused on the major gene-rich region ("1S0.8 region") and identified 75 useful genes along with 93 RFLP markers by comparing 35 different maps of Poaceae species. The RFLP markers were tested by gel blot DNA analysis of wheat group 1 nullisomic-tetrasomic lines, ditelosomic lines, and four single-break deletion lines for chromosome arm 1BS. Seventy-three of the 93 markers mapped to group 1 and detected 91 loci on chromosome 1B. Fifty-one of these markers mapped to two major gene-rich regions physically encompassing 14% of the short arm. Forty-one marker loci mapped to the 1S0.8 region and 10 to 1S0.5 region. Two cDNA markers mapped in the centromeric region and the remaining 24 loci were on the long arm. About 82% of short arm recombination was observed in the 1S0.8 region and 17% in the 1S0.5 region. Less than 1% recombination was observed for the remaining 85% of the physical arm length.

A gene-enriched BAC library for cloning large allele-specific fragments from maize: isolation of a 240-kb contig of the bronze region

A generic bacterial artificial chromosome (BAC) library from a complex plant genome like maize may not be suitable for some types of genomic analysis, for example, for establishing correlations between the genetic and the physical organization of a given chromosome region. Previously, we carried out extensive genetic analysis of the bronze (Bz) region in Zea mays using a W22 inbred line carrying the Bz-McC allele; however, BAC libraries of that line are neither available nor under construction. Here, we report the isolation of large, adjacent BAC clones of this region from a partial BAC library of W22. We developed a BAC vector suitable for cloning NotI fragments and used it to clone size-fractionated genomic DNA that had been cut to completion with the methylation-sensitive, rare-cutting enzyme NotI. This strategy resulted in a very significant enrichment of large genic DNA. From a library of about 20,000 BACs, containing just two-thirds of a maize genome, we isolated 16 BAC clones of the 110-kb distal Bz fragment and 10 BAC clones of the 130-kb proximal Bz fragment. This recovery means that our strategy resulted in a 15- to 24-fold enrichment of specific sequences. The order of the BAC clones in the 240-kb contig, predetermined from an internal NotI site in the Bz-McC allele was confirmed by hybridization with sequences from sites previously mapped proximal and distal to Bz and by sequencing. To show the general utility of our approach and the value of our partial BAC library, we also isolated BAC clones of other sequences, such as tub4 and the complex R-r allele, contained in the same size fraction of DNA. This is the first report of the use of a BAC vector to clone allele-specific large DNA fragments from a plant with a large genome, circumventing the need to construct a complete BAC library.

Interchromosomal recombination in Zea mays

A new allele of the 27-kD zein locus in maize has been generated by interchromosomal recombination between chromosomes of two different inbred lines. A continuous patch of at least 11,817 bp of inbred W64A, containing the previously characterized Ra allele of the 27-kD zein gene, has been inserted into the genome of A188 by a single crossover. While both junction sequences are conserved, sequences of the two homologs between these junctions differ considerably. W64A contains the 7313-bp-long retrotransposon, Zeon-1. A188 contains a second copy of the 27-kD zein gene and a 2-kb repetitive element. Therefore, recombination results in a 7.3-kb insertion and a 14-kb deletion compared to the original S+A188 allele. If nonpairing sequences are looped out, 206 single base changes, frequently clustered, are present. The structure of this allele may explain how a recently discovered example of somatic recombination occurred in an A188/W64A hybrid. This would indicate that despite these sequence differences, pairing between these alleles could occur early during plant development. Therefore, such a somatically derived chimeric chromosome can also be heritable and give rise to new alleles.

Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions

The 78,101 base pair long sequence of a cluster of 22-kDa alpha zein genes in the maize inbred BSSS53 was determined. Each zein gene is contained within a repeat unit that varies in length. If such a repeat, or amplicon, is aligned along the entire sequence, a 10.5-fold sequence amplification is delineated. Because of insertions and deletions in intergenic regions, many of the zein genes are spaced over different distances. Only three out of 10 zein-related sequences have an intact open reading frame, indicating an unusual large number of genes unable to contribute to the accumulation of normal-size 22-kDa zein proteins. It is proposed that the seven remaining zein-related sequences be considered gene reserves because of their potential to be restored by gene conversion. Intergenic insertions in the cluster range from 1098 to 14,896 base pairs. Although they are composed of transposable element sequences, they also contain additional open reading frames, two of them showing homology to rice cDNA sequences. The average amplicon is 4423 base pairs long, with the sequence surrounding each zein gene more than 90% conserved. Coincidently, the size of the amplicon is equivalent to the average gene density (one gene within 4640 bp) in the Arabidopsis thaliana genome, one of the smallest in plants. Successive steps of amplification and insertion of DNA might explain to a certain degree how genome size variation has been generated in plants.

Importance of anchor genomes for any plant genome project

Progress in agricultural and environmental technologies is hampered by a slower rate of gene discovery in plants than animals. The vast pool of genes in plants, however, will be an important resource for insertion of genes, via biotechnological procedures, into an array of plants, generating unique germ plasms not achievable by conventional breeding. It just became clear that genomes of grasses have evolved in a manner analogous to Lego blocks. Large chromosome segments have been reshuffled and stuffer pieces added between genes. Although some genomes have become very large, the genome with the fewest stuffer pieces, the rice genome, is the Rosetta Stone of all the bigger grass genomes. This means that sequencing the rice genome as anchor genome of the grasses will provide instantaneous access to the same genes in the same relative physical position in other grasses (e.g., corn and wheat), without the need to sequence each of these genomes independently. (i) The sequencing of the entire genome of rice as anchor genome for the grasses will accelerate plant gene discovery in many important crops (e.g., corn, wheat, and rice) by several orders of magnitudes and reduce research and development costs for government and industry at a faster pace. (ii) Costs for sequencing entire genomes have come down significantly. Because of its size, rice is only 12% of the human or the corn genome, and technology improvements by the human genome project are completely transferable, translating in another 50% reduction of the costs. (iii) The physical mapping of the rice genome by a group of Japanese researchers provides a jump start for sequencing the genome and forming an international consortium. Otherwise, other countries would do it alone and own proprietary positions.