Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines,as compared to the maize USDA genebank

Key message

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs.

Abstract

Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees–Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees–Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.

     

The binding of host-selective toxin analogs to mitochondria from normal and ;texas' male sterile cytoplasm maize

Tritium-labeled toxin analogs were prepared by reduction with NaB³H₄ of either the toxin from Helminthosporium maydis race T or a toxin component from Phyllosticta maydis. These reduced analogs had high radiochemical specific activities, high biological activities, and plant specificities identical to the native toxins. A filtration assay was developed to test the binding of these labeled analogs to isolated mitochondria. Binding was not energy dependent nor was there measurable matrical uptake. The analogs were shown to be lipophilic, a characteristic which gave rise to considerable nondisplaceable binding. Under conditions limiting nondisplaceable binding, the displaceable binding was shown to be linear with respect to toxin concentration and unsaturable. No significant differences were observed in the binding characteristics between the mitochondria from normal and male-sterile (Texas) cytoplasm maize. The findings suggest that, at physiologically relevant concentrations, these toxin analogs permeate the membranes of susceptible and resistant mitochondria alike. The lack of demonstrable specific binding does not rule out the involvement of a classical receptor site but does indicate that other kinds of molecular interactions may be involved in the mechanisms for toxicity and specificity.     

The structure of cortical cytoplasm

Actin-rich cortical cytoplasm of phagocytic leucocytes forms pseudopodia and controls cell shape and movement by generating directional propulsive and contractile forces. Proteins purified from leucocytes form and deform an actin matrix. Actin-binding protein (ABP) cross-links actin filaments into a three-dimensional lattice with perpendicular branches. This structure, which can be visualized in the electron microscope, is consistent with physical properties of actin-ABP matrices. Gelsolin binds one end of actin filaments with high affinity in the presence of calcium; acumentin, another protein, constitutively binds the other end with low affinity. Together these proteins can control actin filament length and thereby regulate expansion (propulsion) or collapse of the actin network. The assembly state of the network also controls myosin-based contractile forces. A tug-of-war decides the direction of lattice movement, regions of lesser structure tending to move toward regions of greater structure.     

Development of a Brazilian maize core collection

The aim of this study was to evaluate methods for developing a Brazilian maize core collection. For an initial survey of the active collection, passport information, as well as characterization and evaluation of accessions, were taken into consideration, these then being divided according to geographic region and kernel-type. Multiple sampling methods were evaluated. The strategy of constant sampling generated extensive alterations in extract accession frequency. The multivariate strategy with dispersion graphs and principal components associated with the Tocher method was considered efficient for identifying the most divergent genotypes. The multivariate strategy generated greater alterations in the variance of traits. The average number of traits revealed few modifications with the various sampling strategies used. Therefore, the active collection could be considered as possessing a satisfactory amount of information for most of its accessions. Moreover, the multivariate strategy generated modifications in the variance of the traits, independent of sampling intensity.     

An S1 episomal gene of maize mitochondria is expressed in male sterile and fertile plants of the S-type cytoplasm

Summary Maize mitochondria of cytoplasmic male sterile (cms-S) plants contain two linear episomes, S1 (6397 bp) and S2 (5453 bp). S1 contains three long open reading frames URF2 (1017 bp), URF3 (2782 bp) and URF4 (768 bp). We have demonstrated that the URF3 sequence of S1 encodes a protein with an apparent molecular weight of 103 kDa which is found in cms-S but undetectable in cms-T, cms-C or normal (fertile) mitochondria. A translational fusion containing the 5 terminus of the lacZ gene and 800 bp of the 3 end of URF3 was isolated from a cms-S mitochondrial genomic library in the expression vector gt11. Polyclonal antibodies raised against the resulting fusion protein immunoprecipitated a 103 kDa polypeptide from among [³⁵S]-methionine-labeled cms-S mitochondrial proteins but not from normal mitochondrial proteins. The mitochondria of fertile F1 plants resulting from a cross between B37 cms-S and Ky21 (universal restorer) contain as much of this 103 kDa protein as is observed in sterile cms-S mitochondria. The mitochondria of fertile cytoplasmic revertants from cms-RD and cms-LM in a WF9 nuclear background also synthesized the 103 kDa protein. We conclude that the URF3 sequence of the S1 episome is expressed in vivo and that the presence of its gene product in maize mitochondria is not sufficient to confer the male sterile phenotype.     

The male sterile G cytoplasm of wild beet displays modified mitochondrial respiratory complexes

Cytoplasmic male sterility (CMS) in higher plants has been mainly studied in cultivated species. In most cases, pollen abortion is linked to the presence of an additional mitochondrial polypeptide leading to organelle dysfunction in reproductive tissues. In wild beet, both CMS and hermaphrodite plants coexist in natural populations. The G cytoplasm is widely distributed along the Western European coast, and previous genetic studies have demonstrated that this cytoplasm confers male sterility in beet. In the present study, we have identified two mutations of G mitochondrial genes, each of which results in the production of a respiratory chain complex subunit with an altered molecular weight; the NAD9 subunit has a C-terminal extension while the COX2 subunit has a truncated C-terminus. NADH dehydrogenase activity was unchanged in leaves, but cytochrome c oxidase activity was reduced by 50%. Moreover, Western blot analyses revealed that alternative oxidase was more abundant in male sterile G plants than in a fertile control (Nv), suggesting that this alternative pathway might compensate for the cytochrome c oxidase deficiency. Implications of respiratory chain changes and a putative link with CMS are discussed.     

Instability of s male-sterile cytoplasm in maize

A number of S male-sterile plants from several shrunken-2 inbred lines were crossed initially with an R138-TR inbred line pollinator carrying the nonrestoring genotype for S sterile cytoplasm. One such cross, involving a male-sterile female parent from inbred line M825, produced, unexpectedly, a number of male-fertile F₁ progeny, along with the expected male-sterile off-spring. Pollen records of plants in F₂, F₃ and F₄ progenies in the exceptional pedigree, and of a variety of testcross and backcross progenies from these male-fertile exceptions, indicate that the exceptional male fertility is not attributable to the action of either dominant or recessive nuclear restorer genes. They are, however, consistent with the hypothesis that the event responsible for the appearance of exceptional male-fertile offspring among progeny of the original cross involved a change from male-sterile to male-fertile condition in the cytoplasm of the male-sterile M825 plant involved as the female parent in this cross. It appears that this plant bore an ear in which there was a relatively early mutational event at the cytoplasmic level resulting in a chimera involving some kernels which carried S male-sterile cytoplasm, and others which carried the mutated fertile cytoplasmic condition. The finding of a number of additional ear chimeras supports this contention.—The evidence suggests that the change from sterile to fertile cytoplasm has occurred in a number of other instances. The male-sterile line M825 is especially prone to this change. These findings are of particular interest because it has heretofore been considered that both S and T types of male-sterile cytoplasm are highly stable.—The data presented here are not sufficient to support the notion that the exceptional event involves a qualitative change, analogous to gene mutation, in a cytoplasmic entity governing the expression of male fertility. It is equally plausible that the exceptional male fertility is the result of occasional transfer of normal cytoplasm through the male germ cells of maintainer parents.     

粘型小麦不育系育性恢复性的细胞遗传学研究

利用5个粘性不育系分别与中国春的二体,1B重双端体及1B°1D^Ⅳ缺四体杂交,调查其F1的育性及其F1减数分裂中期Ⅰ的染色体配对情况和后期Ⅰ出现落后染色体的细胞频率。结果表明：（1）5个不育系与中国春二体杂交F1的自交结实率存在明显差异。中国春的1B重双端体使5个不育系的自交结实率大幅度下降,中国春的1B°1DⅣ缺四体使各不育系表现全不育;（2）5个不育系和3个父本杂交F1减数分裂中期Ⅰ出现单价体细胞的频率与其后期Ⅰ出现落后染色体细胞的频率不存在直接相关;（3）5个不育系与中国春二体的杂交F1自交结实率与其减数分裂中期Ⅰ出现单价体细胞的频率呈正相关。相关系数为0.9695**,与后期Ⅰ出现落后染色体细胞的频率不直接相关。     

The role of cytoplasm in the manifestation of quantitative characters of maize

Intervarietal reciprocal F₁'s and backcrosses were made between varieties of maize to study the cytoplasmic effects on quantitative characters like grain yeild, maturity, plant and ear heights, and number of ears per plant. It was found that the expression of all characters except the number of ears per plant was modified by the cytoplasm. Cytoplasmic effects were explained on the basis of the plasmon-sensitive genes hypothesis.Part of a thesis submitted by the senior author in partial fulfilment of the requirements for the Ph.D. degree of I.A.R.I., New Delhi.     

Probing the structure of cytoplasm

We have used size-fractionated, fluorescent dextrans to probe the structure of the cytoplasmic ground substance of living Swiss 3T3 cells by fluorescence recovery after photobleaching and video image processing. The data indicate that the cytoplasm of living cells has a fluid phase viscosity four times greater than water and contains structural barriers that restrict free diffusion of dissolved macromolecules in a size-dependent manner. Assuming these structural barriers comprise a filamentous meshwork, the combined fluorescence recovery after photobleaching and imaging data suggest that the average pore size of the meshwork is in the range of 300 to 400 A, but may be as small as 200 A in some cytoplasmic domains.     

两类二角山羊草细胞质小麦雄性不育系的细胞学研究

对具有二角山羊草(Aegilops bicornis)细胞质的同质异核1BL／1RS型小麦雄性不育系ms(Ae．bicornis)-5-1和非1BL／1RS不育系ms(Ae．bicornis)一V9125进行了花药发育细胞学分析。幼穗染色体制片显示,1BL／1RS不育系ms(Ae．bicornis)-5—1减数分裂正常,非1BL／1RS不育系ms(Ae．bicornis)-V9125减数分裂期染色体排列不整齐,出现不正常的四分体和含微核的小孢子。花药发育的细胞学观察表明,1BL／1RS不育系ms(Ae．bicornis)-5—1表现为染败,花药各壁层的发育是正常的;BC3代的非1BL／1RS不育系ms(Ae．bicornis)-V9125表现为园败,且发生了药室合并现象,从细胞学角度证明了二角型小麦不育系存在两个核质互作不育系统。     

urf13-T of T cytoplasm maize mitochondria encodes a 13 kD polypeptide

Polyspecific antibody to a 17 amino acid synthetic peptide from the maize T-cytoplasm urf13-T mitochondrial open reading frame immunoprecipitated a 13 kD polypeptide from ³⁵S-methionine incorporations of T cytoplasm maize. Male-fertile, toxin-insensitive mutants in which the urf13-T sequence is deleted do not synthesize the 13 kD polypeptide. A mutant designated T-4, which carries a 5 bp insertion and a premature stop codon, synthesizes a truncated polypeptide, corresponding to an open reading frame of 8.3 kD. Thus the 13 kD polypeptide is trunctated or absent in mutants expressing male fertility and toxin insensitivity in T-cytoplasm maize.USDA-ARS     

Electrochemical structure of the crowded cytoplasm

The current view of the cytoplasm as a 'bustling and well-organized metropolitan city' raises the issue of how physicochemical forces control the macromolecular interactions and transport of metabolites and energy in the cell. Motivated by studies on bacterial osmosensors, we argue that charged cytoplasmic macromolecules are stabilized electrostatically by their ionic atmospheres. The high cytoplasmic crowding (25-50% of cell volume) shapes the remaining cell volume (50-75%) into transient networks of electrolyte pathways and pools. The predicted 'semi-conductivity' of the electrolyte pathways guides the flow of biochemical ions throughout the cytoplasm. This metabolic and signaling current is powered by variable electrochemical gradients between the pools. The electrochemical gradients are brought about by cellular biochemical reactions and by extracellular stimuli. The cellular metabolism is thus vectorial not only across the membrane but also throughout the cytoplasm.     

The identification of duplicate accessions within a rice germplasm collection using RAPD analysis

A set of accessions of Oryza sativa from the International Rice Research Institute (Philippines) that included known and suspected duplicates as well as closely related germplasm has been subjected to RAPD analysis. The number of primers, the number of polymorphic bands and the total number of bands were determined that will allow the accurate discrimination of these categories of accessions, including the identification of true and suspected duplicates. Two procedures have been described that could be employed on a more general basis for identifying duplicates in genetic resources collections, and further discussion on the values of such activities is presented.     

Guidelines for establishing a culture collection within a biotechnology company

Culture collections within large pharmaceutical and biological companies act as depositories for preserving and maintaining important strains owned by, on the premises of, or sought on behalf of, the company. Other functions of a culture collection include: (a) regulating the flow of cultures into and out of the company; (b) recording and documenting such transfers; and (c) characterizing and/or identifying strains used for research, publications and patents. A culture collection within a biotechnology company is often required to maintain a diverse group of both prokaryote and eukaryote recombinant and non-recombinant strains. All strains and plasmids must be carefully characterized and preserved. A microbiologist with a strong background in microbial physiology, genetics and taxonomy is usually responsible for supervising the culture collection. This article focuses on guidelines for establishing a culture collection in biotechnology companies to serve the needs of both the scientist and the company.     

The effect of sterile conditions on the survival of maize kernels in cold soil

Zkou?ka za chladu u dvou linií kuku?ice p?i st?ídavém obměňování sterility obilek a zeminy ukázale, ?e u daného osiva a zeminy ú?astní se na odumírání obilek v chladné p?dě největ?ím podilem epifytní pathogenní mikroflora, men?ím podílem pak pathogenní mikroflora p?dní a kone?ně nejmen?ím podílem p?ímý ú?inek chladu.     

Effects of Petunia cytoplasmic male sterile (CMS) cytoplasm on the development of sterile and fertility-restored P. parodii anthers

The developmental defects causing cytoplasmic male sterility in Petunia parodii are described in isonuclear fertile, sterile, and fertility-restored plants using both light- and scanning electron microscopy. The aberrant development of the sporogenous tissue and tapetal layer caused by the cytoplasmic male sterile cytoplasm in both Petunia hybrida and P. parodii nuclear backgrounds is similar in onset and progression. The degeneration of the sporogenous tissue and tapetal layer of sterile anthers is first apparent late in meiosis and results in highly abnormal sterile sporogenous tissue by tetrad stage of fertile anthers. The stomium and endothecium do not show major developmental differences between fertile and sterile anthers, but the inner connective tissue of sterile anthers contained calcium crystals not found at high abundance in fertile anthers. Ovoid bodies containing magnesium and phosphorus were seen only in the vascular bundles of fertile anthers. Material prepared for the scanning electron microscope by freeze drying showed better retention of fragile morphological features, while critical-point drying permitted examination of nonvolatile structures, such as cell walls.