Identification of opaque-2 genotypes in segregating populations of Quality Protein Maize by analysis of restriction fragment length polymorphisms

Quality Protein Maize (QPM) is a name given to genetically modified opaque-2 maize with hard endosperm. The opaque-2 mutation conditions a reduction in the amount of zein seed storage protein; zeins are deficient in the essential amino acids lysine and tryptophan, and mutant seed have a higher nutritional value. To utilize the potential of opaque-2 maize, elite inbreds can be converted to o2/o2 forms and subsequently to hard endosperm opaque-2. Since opaque-2 is recessive and endosperm specific, conventional backcross procedures to convert elite inbreds to opaque-2 forms are inefficient. To alleviate this problem, a marker-assisted selection procedure was developed for the Texas A&M University Quality Protein Maize breeding program. Hybridization of an O2 cDNA probe to blots of DNA from plants carrying O2 and o2 alleles showed that restriction fragment length polymorphisms (RFLPs) exist between the W64A o2 allele and O2 alleles of Mo17 and TX5855 inbred lines. To identify the opaque2 genotypes in segregating populations, an RFLP marker assay combining the O2 cDNA probe and HindIII-digestion of genomic DNA was developed. The effectiveness of the O2 RFLP marker assay was tested under field conditions using F₂ and backcross populations of several hard endosperm opaque-2 lines. A comparison of the genotypes identified by RFLP analysis with the seed phenotypes of the next generation indicated that this procedure is accurate and can be used for identifying O2/O2, O2/o2, and o2/o2 genotypes of individual juvenile plants in breeding populations.     

Storage Protein Synthesis in Maize: II. Reduced Synthesis of a Major Zein Component by the Opaque-2 Mutant of Maize

Two zein proteins (Z1 and Z2) represent the majority of the protein synthesized during maize endosperm development. Undegraded membrane-bound polysomes isolated from normal maize synthesized these proteins when incubated in a cell-free protein-synthesizing system from wheat germ. The proteins synthesized in vitro were similar to authentic zein in ethanol solubility and electrophoretic mobility. Zein synthesis was associated with large size classes of membrane bound polysomes in normal maize.Membrane-bound polysomes isolated from developing kernels of opaque-2 mutant synthesized less total zein in vitro, and dramatically reduced incorporation into the Z1 component. The reduction in total zein corresponded to a 50% reduction in the level of membrane-bound polysomes in opaque-2, and the near absence of the large polysome size classes, which synthesized zein in normal maize. We concluded that the opaque-2 mutation results in a decreased "availability" of the zein mRNAs, reflected in a reduced level of membrane-bound polysomes.     

Temporal profiling of essential amino acids in developing maize kernel of normal,opaque - 2 and QPM germplasm

Maize, an important cereal crop, has a poor quality of endosperm protein due to the deficiency of essential amino acids, especially lysine and tryptophan. Discovery of mutants such as opaque-2 led to the development of nutritionally improved maize with a higher concentration of lysine and tryptophan. However, the pleiotropic effects associated with opaque-2 mutants necessitated the development of nutritionally improved hard kernel genotype, the present-day quality protein maize (QPM). The aim of present study was to analyze and compare the temporal profile of lysine and tryptophan in the developing maize kernel of normal, opaque-2 and QPM lines. A declining trend in protein along with tryptophan and lysine content was observed with increasing kernel maturity in the experimental genotypes. However, opaque-2 retained the maximum concentration of lysine (3.43) and tryptophan (1.09) at maturity as compared to QPM (lysine-3.05, tryptophan-0.99) and normal (lysine-1.99, tryptophan-0.45) lines. Opaque-2 mutation affects protein quality but has no effect on protein quantity. All maize types are nutritionally rich at early stages of kernel development indicating that early harvest for cattle feed would ensure a higher intake of lysine and tryptophan. Two promising lines (CML44 and HKI 1105) can be used for breeding high value corn for cattle feed or human food in order to fill the protein inadequacy gap. Variation in lysine and tryptophan content within QPM lines revealed that differential expression of endosperm modifiers with varying genetic background significantly affects nutritional quality, indicating that identification of alleles affecting amino acid composition can further facilitate QPM breeding program.     

Genetic analysis of amino acid accumulation in opaque-2 maize endosperm

The opaque-2 mutation in maize (Zea mays) is associated with an increased level of free amino acids (FAA) in the mature endosperm. In particular, there is a high concentration of lysine, the most limiting essential amino acid. To investigate the basis for the high-FAA phenotype of opaque-2 maize, we characterized amino acid accumulation during endosperm development of several wild-type and opaque-2 inbreds. Oh545o2 was found to have an exceptionally high level of FAA, in particular those derived from aspartate (Asp) and intermediates of glycolysis. The FAA content in Oh545o2 is 12 times greater than its wild-type counterpart, and three and 10 times greater than in Oh51Ao2 and W64Ao2, respectively. We crossed Oh545o2 to Oh51Ao2 and analyzed the F(2:3) progeny to identify genetic loci linked with the high FAA level in these mutants. Quantitative trait locus mapping identified four significant loci that account for about 46% of the phenotypic variance. One locus on the long arm of chromosome 2 is coincident with genes encoding a monofunctional Asp kinase 2 and a bifunctional Asp kinase-homo-Ser dehydrogenase-2, whereas another locus on the short arm of chromosome 3 is linked with a cytosolic triose phosphate isomerase 4. The results suggest an alternation of amino acid and carbon metabolism leads to overproduction and accumulation of FAA in opaque-2 mutants.     

Genetic basis of kernel nutritional traits during maize domestication and improvement

The nutritional traits of maize kernels are important for human and animal nutrition, and these traits have undergone selection to meet the diverse nutritional needs of humans. However, our knowledge of the genetic basis of selecting for kernel nutritional traits is limited. Here, we identified both single and epistatic quantitative trait loci (QTLs) that contributed to the differences of oil and carotenoid traits between maize and teosinte. Over half of teosinte alleles of single QTLs increased the values of the detected oil and carotenoid traits. Based on the pleiotropism or linkage information of the identified single QTLs, we constructed a trait–locus network to help clarify the genetic basis of correlations among oil and carotenoid traits. Furthermore, the selection features and evolutionary trajectories of the genes or loci underlying variations in oil and carotenoid traits revealed that these nutritional traits produced diverse selection events during maize domestication and improvement. To illustrate more, a mutator distance–relative transposable element (TE) in intron 1 of DXS2, which encoded a rate‐limiting enzyme in the methylerythritol phosphate pathway, was identified to increase carotenoid biosynthesis by enhancing DXS2 expression. This TE occurs in the grass teosinte, and has been found to have undergone selection during maize domestication and improvement, and is almost fixed in yellow maize. Our findings not only provide important insights into evolutionary changes in nutritional traits, but also highlight the feasibility of reintroducing back into commercial agricultural germplasm those nutritionally important genes hidden in wild relatives.     

Transaminase GOT and GPT activity in extirped sprouts of normal and opaque-2 Maize (Zea mays L.) seedlings

The increased activity of GOT (E.C.2.6.1.1.) and GPT (E.C.2.6.1.2.) transaminases in maize seedlings found as a marker of genotype opaque-2, was investigated in extirped sprouts of both genotypes, normal and opaque-2. The enzymatic activity was determined in three maize samples from breeding experiments, each sample consisting of a genotype pair, normal and opaque-2, collected from segregating ears of maize plants in the S₁ generation. The seedlings were aseptically grown for 7 days in two variants of cultivation, intact seedlings and sprouts extirped after 4 days of germination. In the intact seedlings of genotype opaque-2 an increased activity of GOT and GPT, as compared to the intact normal plants, was observed. The extirpation of the sprouts enhanced GOT and GPT activity in the sprouts of both genotypes. However, in extirped sprouts the GOT and GPT activity was found to be still higher in the genotype opaque-2 as compared with the sprouts of normal genotype. Thus it seems that the increased transaminase activity in the sprouts of genotype opaque-2 is genetically determined. The increase does not result from an induction of enzyme synthesis through the supply of amino acids translocated from the endosperm to the sprouts. The absolute level of transaminases in the different breeding samples is dependent on the parenteral lines, the relative level of GOT and GPT activities is higher in the genotype opaque-2.     

Characterization of polysomes and incorporation in vitro of leucine and lysine in normal and opaque-2 zea mays endosperm during development

Polysome preparations obtained from opaque-2 and normal maize endosperms during development did not show any significant difference in sedimentation coefficient or nucleotide composition. The pattern of incorporation in vitro of lysine and leucine, however, differed quite distinctly in these two preparations. During early stages of maturity the polysomes from opaque-2 incorporated substantially more lysine and less leucine as compared with those from normal maize. Although the trend was reversed at 25 days post-pollination, this did not result in any significant zein accumulation since very little total protein was synthesized after that stage in opaque-2 maize endosperm. It is, therefore, suggested that the opaque-2 gene exerts a regulatory control on mRNA synthesis, required for zein formation at early stages of maturation.     

New Methods for Extraction and Quantitation of Zeins Reveal a High Content of gamma-Zein in Modified opaque-2 Maize

We have developed methods for quantitative extraction and analysis of zeins from maize (Zea mays L.) flour. Extraction involved solubilization of total endosperm proteins in an alkaline buffer containing SDS and 2-mercaptoethanol with subsequent precipitation of nonzein proteins by the addition of ethanol to 70%. Analysis of these proteins by SDS-PAGE with Coomassie blue staining and by Western blotting and ELISA assay with zein antibodies revealed that this extraction method is more quantitative than the traditional Landry-Moureaux procedure, especially for the β- and γ-zeins. This method was used to extract and analyze the zein content of several `Quality Protein Maize' (QPM) varieties developed by the International Maize and Wheat Improvement Center. QPM varieties contain `modifier genes' that confer a vitreous phenotype on opaque-2 genotypes, while maintaining the elevated levels of lysine and tryptophan characteristic of this mutant. This analysis revealed that the QPM types contain 2 to 4 times the amount of the γ-zein than unmodified opaque-2 or normal maize varieties. Possible relationships between the high expression of the γ-zein and the modified opaque phenotype are discussed.     

Genomic Organization of α-Amylase Gene in High Lysine Opaque-2 Maize

Genomic DNA was isolated from 7-day old etiolated seedlings of normal and high lysine opaque-2 maize and purified by CsCl gradient. Purified DNA was found to be ～48.5 kb in size. Restriction analysis of genomic DNA with EcoRI and HindIII did not reveal any noticeable difference between normal and opaque-2 DNA. Southern blot analysis, using α-amylase probe, showed multiple bands. One of the hybridizing bands (～4 kb) of genomic DNA was more intense in opaque-2 than in normal. This DNA was cloned into pUC 18 plasmid and presence of α-amylase was confirmed by Southern hybridization using α-amylase probe.     

Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication

Phenotypic variation on which selection can act during evolution may be caused by variation in activity level of developmental regulatory genes. In many cases, however, such genes affect multiple traits. This situation can lead to co-evolution of traits, or evolutionary constraint if some pleiotropic effects are detrimental. Here, we present an analysis of quantitative traits associated with gene copy number of two important maize regulatory genes, the duplicate FLORICAULA/LEAFY orthologs zfl1 and zfl2. We found statistically significant associations between several quantitative traits and copy number of both zfl genes in several maize genetic backgrounds. Despite overlap in traits associated with these duplicate genes, zfl1 showed stronger associations with flowering time, while zfl2 associated more strongly with branching and inflorescence structure traits, suggesting some divergence of function. Since zfl2 associates with quantitative variation for ear rank and also maps near a quantitative trait locus (QTL) on chromosome 2 controlling ear rank differences between maize and teosinte, we tested whether zfl2 might have been involved in the evolution of this trait using a QTL complementation test. The results suggest that zfl2 activity is important for the QTL effect, supporting zfl2 as a candidate gene for a role in morphological evolution of maize.     

An analysis of genetic diversity across the maize genome using microsatellites

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.     

Ribonuclease Activity in Normal, opaque-2, and floury-2 Maize Endosperm during Development

The elevated ribonuclease activity produced in the endosperm of a maize (Zea mays L.) inbred, W64A, by homozygous opaque-2, results from a more than doubled rate of ribonuclease accumulation occurring prior to 16 days post-pollination; after 16 days the rates in opaque-2 and normal are the same, suggesting that opaque-2 is no longer active. The pattern of ribonuclease increase in the opaque-2 dosage series indicates that opaque-2 is not fully recessive. Ribonuclease accumulation is not affected by floury-2 in a second inbred, B14. The results are discussed with reference to other proteins, notably zein, the net synthesis of which is affected by opaque-2.     

Identification of functional genetic variations underlying drought tolerance in maize using SNP markers

Single nucleotide polymorphism (SNP) is a common form of genetic variation and popularly exists in maize genome. An Illumina GoldenGate assay with 1 536 SNP markers was used to genotype maize inbred lines and identified the functional genetic variations underlying drought tolerance by association analysis. Across 80 lines, 1 006 polymorphic SNPs (65.5% of the total) in the assay with good call quality were used to estimate the pattern of genetic diversity, population structure, and familial relatedness. The analysis showed the best number of fixed subgroups was six, which was consistent with their original sources and results using only simple sequence repeat markers. Pairwise linkage disequilibrium (LD) and association mapping with phenotypic traits investigated under water-stressed and well-watered regimes showed rapid LD decline within 100-500 kb along the physical distance of each chromosome, and that 29 SNPs were associated with at least two phenotypic traits in one or more environments, which were related to drought-tolerant or drought-responsive genes. These drought-tolerant SNPs could be converted into functional markers and then used for maize improvement by marker-assisted selection.     

湿加松无性系表型遗传多样性研究

以35个湿加松（Pinus elliottii×P.caribaea Morelet var.hondurensis）无性系为试验材料,对其8个表型性状进行相关性分析、聚类分析及主成分分析研究,并深入探讨了遗传多样性水平,为湿加松无性系利用及良种选育提供科学依据。结果表明：（1）生长性状变异系数介于12.31~29.28%,均值为22.90%;多样性指数介于1.61~1.80,均值为1.69。形质性状变异系数介于13.34~47.25%,均值为26.86%;多样性指数介于1.50~1.94,均值为1.77。表明湿加松无性系遗传变异较为丰富,遗传多样性水平较高。（2）8对表型性状两两间有11对呈极显著正相关,5对呈显著正相关。选定材积为该材料育种选择的主要指标,其次为树高。（3）采用系统聚类法在欧式距离为12的时候将35个无性系分为6大类群,部分来源相同或父本相同的聚为一类,说明它们在表型上的变异较小。（4）针对8个表型性状做主成分分析提取了3个主成分,累积贡献率达86.00%,主要代表了6个性状,以此来表达所有供试材料的综合变异情况。     

Purification and characterization of proteolytic enzymes from normal and opaque-2Zea mays L. developing endosperms

Purification and characterization of proteases from developing normal maize endosperm and high lysine opaque-2 maize endosperm have been carried out with a view to understand their role in storage protein modification. At day 15, normal maize endosperm had two types of proteolytic enzymes, namely, protease I and protease II, while at day 25 protease n disappeared and in place protease III appeared. However, in opaque-2 maize endosperm at both the stages only one type of enzyme (protease I) was present. These proteases had many properties in common-optimum pH and temperature were respectively, 5.7and 40°C; their activity was inhibited to the extent of 75 –93 % by p-chloromercuribenzoate; trypsin inhibitor inhibited the activity more at early stages of endosperm development; all proteases cleaved synthetic substrates p-tosyl-L-arginine methylesler and N-benzoyl-L-tyrosine ethyl ester and poly-L-glutamic acid. TheKm values of day 15 and 25 normal maize endosperm proteases ranged from 2.73–3.30, while for opaque-2 maize endosperm protease I it was 3.33 mg azocasein per ml assay medium. These enzymes, however, differed with respect to proteolytic activity towards poly-L-lysine. Only normal maize endosperm protease III at day 25 followed by protease II at day 15 showed high activity towards this homopolypeptide suggesting thereby their role in determining the quality of normal maize endosperm protein. Part of Ph.D. thesis submitted by the first author     

Factor and principal component analyses as alternatives to index selection

Summary Selections from factor and principal component analyses were compared with those from the Smith-Hazel index when selecting for several switchgrass (Panicum virgatum L.) traits. The objective of this study was to examine several alternatives to index selection. Such procedures would potentially eliminate problems of selection associated with Smith-Hazel indices, including errors in genetic parameter estimates and difficulty in assigning relative economic weights to traits. Selection was performed on 1,280 plants that were evaluated over 2 years at 1 location, in a randomized complete block design with 4 replicates. The plants were evaluated for forage yield and several forage quality traits. The comparisons of index selection with principal factor analysis, maximum-likelihood factor analysis and principal component analysis were made for three sets of traits (five traits per set) to estimate repeatability for the comparisons. Multivariate analyses were performed on both simple and genotypic correlation matrices. Comparisons were made by computing Spearman's rank correlations between selection index plant scores and scores computed from multivariate analysis and by determining the number of plants selected in common for the selection methods. Among the three multivariate analysis methods evaluated in this study, principal component analysis had the highest correlation with index selection. The high correlation for principal component analysis of simple correlation matrices indicates the potential for using this statistical method for selection purposes. This would permit the breeder to reduce field costs (e.g., time, labor, equipment) required to obtain the genetic parameter estimates necessary to construct selection indices.     

Study of the alcohol-soluble protein of corn by electrophoresis in PAAG]

An electrophoretic study of zein in 115 lines of common maize resulted in detecting 7 types of spectra. The analysis of opaque-2 sources showed that they differ between each other in the number and component composition, similar to the norm. The study of isogenic lines revealed that in different genotypes the gene opaque-2 behaves unsynonymously: it either does not influence the component composition of zein or changes it qualitatively.     

A test of the hypothesis that correlational selection generates genetic correlations

Theory predicts that correlational selection on two traits will cause the major axis of the bivariate G matrix to orient itself in the same direction as the correlational selection gradient. Two testable predictions follow from this: for a given pair of traits, (1) the sign of correlational selection gradient should be the same as that of the genetic correlation, and (2) the correlational selection gradient should be positively correlated with the value of the genetic correlation. We test this hypothesis with a meta-analysis utilizing empirical estimates of correlational selection gradients and measures of the correlation between the two focal traits. Our results are consistent with both predictions and hence support the underlying hypothesis that correlational selection generates a genetic correlation between the two traits and hence orients the bivariate G matrix.     

是金子无论在何处都发光: 玉米和水稻驯化中的趋同选择

野生植物的驯化为人类定居与文明起源奠定了重要基础。在世界范围内不同地区生活的古人类分别对当地不同的野生植物进行了驯化, 而经过驯化的作物常常表现出相似的驯化综合性状。在基因组层面上对趋同选择规律的解析, 可为作物育种提供重要信息与遗传资源。近日, 中国农业大学杨小红/李建生和华中农业大学严建兵领衔的团队从单基因和全基因组2个层次系统解析了玉米(Zea mays)和水稻(Oryza sativa)趋同选择的遗传基础, 发现玉米KRN2与水稻OsKRN2受到了趋同选择, 并通过相似的途径调控玉米与水稻的粒数与产量。他们还发现玉米与水稻在全基因组范围内存在大量趋同选择同源基因对(gene pair), 这些基因在淀粉代谢、糖及辅酶合成等途径特异富集。该研究不仅克隆了在玉米与水稻中均具有重要育种价值的趋同选择同源基因对KRN2/OsKRN2, 而且在全基因组水平上揭示了玉米与水稻趋同选择的规律, 为进一步解析驯化综合性状形成的分子机理及其在育种中的应用奠定了重要理论基础。