Teosinte crossing barrier1, a locus governing hybridization of teosinte with maize

A teosinte gene or gene cluster, Teosinte crossing barrier1 (Tcb1), that restricts crossability with maize mapped 6 centiMorgans distal to sugary-1 on chromosome 4. Tcb1 is loosely linked with the gametophyte-1 locus whose Ga1-s allele, present in many popcorns, confers nonreceptivity to the pollen of other maize varieties (ga1). Full-strength Tcb1 (positive modifiers present) was nonreceptive to Ga1-s as well as to ga1 pollen. Attenuated Tcb1 (positive modifiers absent) was detectably more receptive to Ga1-s than to ga1, suggesting cross recognition between the two systems of incompatibility. Reciprocally, homozygous Ga1-s was unreceptive both to Tcb1 and tcb1 pollen, but heterozygous Ga1-s/ga1 plants were somewhat more receptive to Tcb1 than to tcb1. Discrimination by Tcb1/− females against tcb1 pollen is prezygotic, accomplished without the loss of viable ovules. When introduced into maize, Tcb1 incompatibility may be useful for isolating one category of commercial varieties from another. Received: 25 September 2000 / Accepted: 24 November 2000     

Geographic distribution of alleles at the Ga2 locus for segregation distortion in barley

Summary A distorted segregation of esterase alleles at the complex loci, Est1, Est2 and Est4, was found in an F₂ population. This distortion is typical for cross combinations between the Ga2Ga2 and ga2ga2 genotypes responsible for segregation distortion, since the Ga2 locus is linked with the complex loci encoding the esterase isozymes. The segregation of esterase isozyme patterns in F₂ populations between 473 varieties of barley and a tester of ga2ga2 genotype was examined, and the genotypes inducing segregation distortion were detected. Varieties with a ga2ga2 genotype are widely distributed throughout the world, whereas Ga2Ga2 varieties are found only in eastern and southern regions of Asia, from Japan to North India, with a low frequency. In varieties collected from these regions, some associations were detected between alleles at the Ga2 locus and esterase isozyme patterns. Additionally, most of the Ga2 barley varieties are naked and possess a BtBtbt2bt2 genotype for a non-brittle rachis.     

Identification and fine mapping of <Emphasis Type="Italic">S-d</Emphasis>, a new locus conferring the partial pollen sterility of intersubspecific F<Subscript>1</Subscript> hybrids in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The partial pollen abortion of hybrids between the indica and japonica subspecies of Asian cultivated rice is one of the major barriers in utilizing intersubspecific heterosis in hybrid rice breeding. Although a single hybrid pollen sterility locus may have little impact on spikelet fertility, the cumulative effect of several loci usually leads to a serious decrease in spikelet fertility. Isolating of the genes conferring hybrid pollen sterility is necessary to understand this phenomenon and to overcome the resulting genetic barrier. In this study, a new locus for F₁ pollen sterility, S-d, was identified on the short arm of chromosome 1 by analyzing the genetic effect of substituted segments of the near-isogenic line E11-5 derived from the japonica variety Taichung 65 (recurrent parent) and the indica variety Dee-geo-woo-gen (donor parent). The S-d locus was first mapped to a 0.8 cM interval between SSR markers PSM46 and PSM80 using a F₂ population of 125 individuals. The flanking markers were then used to identify recombinants from a population of 2,160 plants derived from heterozygotes of the primary F₂ population. Simultaneously, additional markers were developed from genomic sequence divergence in this region. Analysis of the recombinants in the region resulted in the successful mapping of the S-d locus to a 67-kb fragment, containing 17 predicted genes. Positional cloning of this gene will contribute to our understanding of the molecular basis for partial pollen sterility of intersubspecific F₁ hybrids in rice.     

ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize

The number of pollen grains is a critical determinant of reproductive success in seed plants and varies among species and individuals. However, in contrast with many mutant-screening studies relevant to anther and pollen development, the natural genetic basis for variations in pollen number remains largely unexplored. To address this issue, we carried out a genome-wide association study in maize, ultimately revealing that a large presence/absence variation in the promoter region of ZmRPN1 alters its expression level and thereby contributes to pollen number variation. Molecular analyses showed that ZmRPN1 interacts with ZmMSP1, which is known as a germline cell number regulator, and facilitates ZmMSP1 localization to the plasma membrane. Importantly, ZmRPN1 dysfunction resulted in a substantial increase in pollen number, consequently boosting seed production by increasing female–male planting ratio. Together, our findings uncover a key gene controlling pollen number, and therefore, modulation of ZmRPN1 expression could be efficiently used to develop elite pollinators for modern hybrid maize breeding.     

Genetic and cellular analysis of cross-incompatibility in Zea mays

Three genetic systems conferring cross-incompatibility have been described in Zea mays: Teosinte crossing barrier1-strong (Tcb1-s) found in teosinte, and Gametophyte factor1-strong (Ga1-s) and Ga2-s found in maize and teosinte. The reproductive barrier between maize and some weedy teosintes is controlled by the Tcb1-s locus. Multi-generation inheritance experiments on two independent Tcb1-s lineages show that the Tcb1-s barrier is unstable in some maize lines. Reciprocal crosses between Tcb1-s tester plants and three recombinants in the Tcb1-s mapping region demonstrate that the Tcb1-s haplotype contains separable male and female components. In vivo assays of the dynamics of pollen tube growth and pollen tube morphology during rejection of incompatible pollen in silks carrying the Tcb1-s, Ga1-s, or Ga2-s barriers showed that, in all three, pollen tube growth is slower than in compatible crosses at early stages and had ceased by 24 h after pollination. In all three crossing barrier systems, incompatible pollen tubes have clustered callose plugs in contrast to pollen tubes of compatible crosses. Incompatible pollen tubes growing in the Tcb1-s, Ga1-s, and Ga2-s silks have different morphologies: straight, curved, and kinked, respectively. The distinct morphologies suggest that these crossing barriers block incompatible pollen through different mechanisms. This study lays the foundation for cloning the Tcb1 genes and provides clues about the cellular mechanisms involved in pollen rejection in the Tcb1-s, Ga1-s, and Ga2-s crossing barriers.     

Cytological mechanism of pollen abortion resulting from allelic interaction of F1 pollen sterility locus in rice (Oryza sativa L.)

Pollen abortion is one of the major reasons causing the inter-subspecific F₁ hybrid sterility in rice and is due to allelic interaction of F₁ pollen sterility genes. The microsporogenesis and microgametogenesis of Taichung 65 and its three F₁ hybrids were comparatively studied by using techniques of differential interference contrast microscopy, semi-thin section light microscopy, epifluorescence microscopy and TEM. The results showed that there were differences among the cytological mechanisms of pollen abortion due to allelic interaction at the three F₁ pollen sterility loci. The allelic interaction at S-a locus resulted in microspores unable to extend the protoplasm membrane with the enlargement of the microspore at the middle microspore stage and finally producing empty abortive pollen. The allelic interaction at S-b locus caused asynchronous development of microspores at the middle microspore stage producing stainable abortive pollen. The allelic interaction at S-c locus mainly led to the non-dissolution of the generative cell wall and finally caused the hybrid F₁ mainly producing stainable abortive pollen. Genotypic identification indicated that the abortive pollen were those with S ^j allele.     

Genetic basis of low-temperature-sensitive sterility in indica-japonica hybrids of rice as determined by RFLP analysis

 Low-temperature-sensitive sterility (LTSS) has become one of the major obstacles in indica-japonica hybrid rice breeding. In this study, we determined, using RFLP markers, the genetic basis of LTSS in two populations derived from crosses between indica and japonica parents, the BC₁F₁ of 3037/02428//3037 and the F₂ of 3037/02428. The fertility segregation in the two populations under low-temperature conditions was used as a measurement of the temperature sensitivity of the various genotypes in the populations. A RFLP survey of bulked extremes from the BC₁F₁ population identified three genomic regions, two on chromosome 1 and one on chromosome 12, that were likely to contain genes for LTSS (or Ste loci). One-way ANOVA and QTL analysis using a total of 19 markers from these three genomic regions resolved three Ste loci in the BC₁F₁ population and two Ste loci in the F₂ population. On the basis of chromosomal location these loci were distinct from those governing wide-compatibility identified in previous studies. Two- and three-way ANOVA showed that these loci acted essentially independent of each other in conditioning LTSS. The main mode of gene action was an interaction between the indica and the japonica alleles within each locus. For each respective locus this resulted in a drastic fertility reduction in the heterozygote state relative to the homozygote state. The results have significant implications in indica-japonica hybrid rice breeding programs. Received : 10 April 1996 / Accepted: 2 June 1997     

Identification of neutral alleles at pollen sterility gene loci of cultivated rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) from wild rice (<Emphasis Type="Italic">O. rufipogon</Emphasis> Griff.)

Oryza rufipogon Griff. is the ancestor of Asian cultivated rice (O. sativa L.) and possesses valuable genes for rice breeding. Pollen abortion is one of the major causes of indica–japonica hybrid sterility in rice and it happens due to allelic interaction at the pollen sterility gene loci. A total of six loci (Sa, Sb, Sc, Sd, Se, and Sf) have been found to be associated with F₁ pollen sterility between indica and japonica rice, and five of them (all except Sf) have been mapped. Neutral alleles (S ⁿ ) at each locus have the potential to overcome the pollen sterility associated with the respective locus. Therefore, exploitation and utilization of neutral alleles have significant importance in overcoming indica–japonica hybrid sterility. In this study, an accession (IRW28) of O. rufipogon, native to China, was selected as paternal to cross with typical japonica (Taichung 65) and indica (Guanglu’ai 4) tester lines, and two F₂ populations were developed. The simple sequence repeat markers tightly linked to five pollen sterility loci were applied for genotyping the F₂ populations. Chi-squared tests were applied to examine the normal segregation/distortion at each locus. The expected and observed pollen sterility for each locus were estimated. As a result, the genotypes at five pollen sterility gene loci for IRW28 were identified as: Sa ⁱ⁻¹/Sa ⁱ⁻¹, Sb ⁿ /Sb ⁿ , Sc ⁱ⁻²/Sc ⁱ⁻², Sd ⁿ /Sd ⁿ and Se ⁿ /Se ⁿ . Our results suggest that IRW28 (O. rufipogon) has the neutral alleles for pollen fertility at the Sb, Sd and Se loci, and these alleles have a good affinity with indica and japonica rice. These neutral alleles provide valuable gene resources to overcome the inter-subspecific hybrid pollen sterility in rice.     

Genetic dissection of embryo sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice

The partial sterility of hybrids has been a major barrier for utilization of the strong heterosis expressed in hybrids between Oryza sativa ssp. indica and O. sativa ssp. japonica. Wide-compatibility varieties, comprising a special class of germplasm, are able to produce fertile hybrids when crossed to both indica and japonica varieties. However, all the work on wide compatibility and majority of studies on indica/japonica hybrid sterility reported so far were based only on spikelet fertility; thus, it is not known to what extent male and female gamete abortions influence hybrid sterility. In this study, we investigated pollen fertility, embryo sac fertility, and spikelet fertility in an F₁ population of 202 true hybrid plants derived from a three-way cross (02428/Nanjing 11//Balilla). A partial regression analysis showed that the pollen and embryo sac fertility contributed almost equally to spikelet fertility. QTL analysis based on a linkage map of 191 polymorphic marker loci identified two QTLs for pollen fertility, one QTL for embryo sac fertility, and three QTLs for spikelet fertility. The S5 locus, previously identified as a locus for wide compatibility by spikelet fertility analysis, is a major locus for embryo sac fertility, and a QTL on chromosome 5 had a major effect on pollen fertility. These two loci coincided with the two major QTLs for spikelet fertility. The study also detected a QTL on chromosome 8, showing a large effect on spikelet fertility but no effect on either pollen or embryo sac fertility. Very little interaction among the QTLs was detected. The implications of the findings in rice breeding programs are discussed.     

RFLP mapping of the sugary enhancer1 gene in maize

RFLP marker data from an F₂₃ population derived from a cross between a sugary1 (su1) and a sugary enhancer1 (su1, sel) inbred were used to construct a genetic linkage map of maize. This map includes 93 segregating marker loci distributed throughout the maize genome, providing a saturated linkage map that is suitable for linkage analysis with quantitative trait loci (QTL). This population, which has been immortalized in the form of sibbed F₂₃ families, was derived from each of the 214 F₂ plants and along with probe data are available to the scientific community. QTL analysis for kernel sucrose (the primary form of sugar) concentration at 20 days after pollination (DAP) uncovered the segregation of seven major QTL influencing sucrose concentration; a locus linked to umc36a described the greatest proportion of the variation (24.7%). Since maltose concentration has previously been reported to be associated with the se1 phenotype, an analysis of probe associations with maltose concentration at 40 DAP was also conducted. The highly significant association of umc36a with maltose and sucrose concentrations provided evidence that this probe is linked to se1. Phenotypic evaluation for the se1 genotype in each F₂₃ family enabled us to map the gene 12.1 cM distal to umc36a. In contrast to previous work where se1 was reported to be located on chromosome four, our data strongly suggest that the sugary enhancer1 locus maps on the the distal portion of the long arm of chromosome 2 in the maize genome.     

Delimitation of the rice wide compatibility gene S5 n to a 40-kb DNA fragment

Wide compatibility varieties (WCVs) are a special class of rice (Oryza sativa L.) germplasm that produces hybrids with normal pollen and spikelet fertility when crossed with both indica and japonica subspecies. The wide compatibility gene S5 ⁿ has been used extensively in intersubspecific hybrid breeding programs. We previously mapped the S5 locus to a 2.2-cM genomic region between RM253 and R2349 on chromosome 6, using a population of 356 F₁ plants derived from the three-way cross 02428/Nanjing11//Balilla. In this study, a chromosome walking strategy was employed to construct a physical map covering this genomic region using these two closest markers as the starting points. A physical map consisting of six overlapping BAC clones was formed, spanning a genomic region of 540-kb in length. By analyzing recombination events from a population of 8,000 F₁ plants derived from a three-way cross based on near isogenic lines of the S5 locus, the S5 locus was localized to a DNA fragment of 40-kb in length, flanked by two shotgun subclones, 7B1 and 15D2. Sequence analysis of this fragment predicted five open reading frames, encoding xyloglucan fucosyltransferases, dnak-type molecular chaperone BiP, a putative eukaryotic aspartyl protease, and a hypothetical protein. This result will be very useful in molecular cloning of the S5 ⁿ allele and marker-assisted transferring of the wide compatibility gene in rice breeding programs.     

Identification of a maize linkage group related to apomixis in Brachiaria

 A bulked segregant analysis using RFLPs and RAPDs was carried out to identify molecular markers co-segregating with apomixis in a Brachiaria F₁ population. The test population used was a cross between sexual B. ruziziensis R44 and the aposporous apomictic Brachiaria brizantha cv Marandu. The Brachiaria genome was systematically scanned using 61 cDNA and genomic maize clones detecting 65 loci located at 40 cM, on average, one from each other in the maize genome. The finding of a clone that presented a polymorphic band co-segregating with apomixis (umc147) led to the identification of another marker within the same area (umc72). The clones belong to a duplicated linkage group that maps to the distal part of maize chromosome-1 long arm and chromosome-5 short arm. RAPD analysis using 184 primers from Operon sets yielded one more marker (OPC4) significantly linked to the trait mapping the same locus. OPC4 had been previously reported as a potential marker for apospory in Pennisetum. A map of the region was constructed using additional clones that belong to the same maize linkage group. Since that was the only genomic region that presented an apomixis-linked polymorphism our observations support the existence of a single locus directing apospory in Brachiaria. Received: 9 September 1996 / Accepted: 20 September 1996     

A farnesyl pyrophosphate synthase gene expressed in pollen functions in S‐RNase‐independent unilateral incompatibility

Multiple independent and overlapping pollen rejection pathways contribute to unilateral interspecific incompatibility (UI). In crosses between tomato species, pollen rejection usually occurs when the female parent is self‐incompatible (SI) and the male parent self‐compatible (SC) (the ‘SI × SC rule’). Additional, as yet unknown, UI mechanisms are independent of self‐incompatibility and contribute to UI between SC species or populations. We identified a major quantitative trait locus on chromosome 10 (ui10.1) which affects pollen‐side UI responses in crosses between cultivated tomato, Solanum lycopersicum, and Solanum pennelliiLA0716, both of which are SC and lack S‐RNase, the pistil determinant of S‐specificity in Solanaceae. Here we show that ui10.1 is a farnesyl pyrophosphate synthase gene (FPS2) expressed in pollen. Expression is about 18‐fold higher in pollen of S. pennellii than in S. lycopersicum. Pollen with the hypomorphic S. lycopersicum allele is selectively eliminated on pistils of the F₁ hybrid, leading to transmission ratio distortion in the F₂ progeny. CRISPR/Cas9‐generated knockout mutants (fps2) in S. pennelliiLA0716 are self‐sterile due to pollen rejection, but mutant pollen is fully functional on pistils of S. lycopersicum. F₂ progeny of S. lycopersicum × S. pennellii (fps2) show reversed transmission ratio distortion due to selective elimination of pollen bearing the knockout allele. Overexpression of FPS2 in S. lycopersicum pollen rescues the pollen elimination phenotype. FPS2‐based pollen selectivity does not involve S‐RNase and has not been previously linked to UI. Our results point to an entirely new mechanism of interspecific pollen rejection in plants.     

Genetic analysis and fine mapping of the Ga1-S gene region conferring cross-incompatibility in maize

Cross-incompatibility genes known as gametophyte factors (ga) are numerous in maize. Many popcorn strains carry these genes and cannot be fertilized by pollen of dent and flint maize strains although the reciprocal crosses are successful. A Chinese popcorn strain SDGa25 carries the strongest allele of Ga1 (Ga1-S) and the majority of Chinese dent and flint maize germplasm are incompatible with SDGa25. The incompatibility is due to pollen tube growth obstruction 2 h after pollination. The pollen tube is arrested in the silk segment 5.5 cm distal to the pollination area and never reaches the ovule. The Ga1-S carried by SDGa25 behaves as a single dominant gene. This gene was mapped between markers SD3 on BAC AC200747 0.827 cM apart on the telomere side and SD12 on BAC AC204382 0.709 cM apart on the centromere side. The genetic region mapped spanning the Ga1-S locus was estimated to be 1.5 cM in length and the physical distance is 2,056,343 bp on ctg156 based on the B73 RefGen_v2 sequence. Gametophyte factors influence gene flow direction and the strongest Ga1-S allele is useful for isolating one category of commercial varieties from another. The eight tightly linked markers to Ga1-S developed in this study would greatly improve marker-assisted introgression efficiency and the fine mapping would facilitate the isolation of the Ga1-S.     

Pas1 is a common lung cancer susceptibility locus in three mouse strains

Inherited predisposition to lung cancer is a phenotypic trait shared by different mouse inbred strains that show either a high or an intermediate predisposition. Other strains are instead genetically resistant. The Pas1 locus is the major determinant of lung cancer predisposition in the A/J strain (Gariboldi et al. 1993). To define the determinants of susceptibility to lung tumorigenesis in the highly susceptible SWR/J and in the intermediately susceptible BALB/c mice, we analyzed (BALB/c × SWR/J)F₂ and (BALB/c × C3H/He)F₂ crosses by genetic linkage experiments. The present results provide unequivocal evidence that the same Pas1/+ allele that leads to lung cancer predisposition is shared by A/J, SWR/J, and BALB/c strains. The intermediate susceptibility of the BALB/c strain would result by interaction of Pas1 locus with lung cancer resistance loci. Received: 18 April 1997 / Accepted: 15 June 1997     

Mating system dynamics of Ocotea tenera (Lauraceae), a gynodioecious tropical tree

Progeny arrays of Ocotea tenera (Lauraceae), a gynodioecious tree endemic to Costa Rica, were electrophoretically surveyed for allozyme variation to estimate the outcrossing rate in the overall population and to test for differences in outcrossing rates between hermaphroditic and female trees. Multilocus outcrossing rate estimates across 3 yr indicated O. tenera predominantly outcrosses. However, significant heterogeneity in single-locus outcrossing rates was found among loci. Two loci (Fe1, Fe2) gave high outcrossing estimates, and a third locus (Gdh) gave much lower outcrossing estimates. Heterogeneity in Gdh pollen allele frequencies, consanguineous matings, and selection against homozygous zygote genotypes at the Fe1 and Fe2 loci are factors contributing to the discrepancy in outcrossing rate estimates among loci. There were no differences in the mating systems of hermaphroditic and female trees, which suggests that factors beyond prevention of self-fertilization may have also promoted the evolution of gynodioecy in O. tenera.     

Genetic analysis of tolerance to low-phosphorus stress in maize using restriction fragment length polymorphisms

Summary An understanding of the genetic nature underlying tolerance to low-phosphorus (low-P) stress could aid in the efficient development of tolerant plant strains. The objective of this study was to identify the number of loci in a maize (Zea mays L.) population segregating for tolerance to low-P stress, their approximate location, and the magnitude of their effect.Seventy-seven restriction fragment length polymorphisms (RFLPs) were identified and scored in a maize F₂ population derived from a cross between line NY821 and line H99. The F₂ individuals were self-pollinated to produce F₃ families. Ninety F₃ families were grown in a sand-alumina system, which simulated diffusion-limited, low-P soil conditions. The F₃ families were evaluated for vegetative growth in a controlled-environment experiment. To identify quantitative trait loci (QTLs) underlying tolerance to low-P stress, the mean phenotypic performances of the F₃ families were contrasted based on genotypic classification at each of 77 RFLP marker loci.Six RFLP marker loci were significantly associated with performance under low-P stress (P<0.01). One marker locus accounted for 25% of the total phenotypic variation. Additive gene action was predominant for all of the QTLs identified. Significant marker loci were located on four separate chromosomes representing five unlinked genomic regions. Two marker loci were associated with an additive by additive epistatic interaction. A multiple regression model including three marker loci and the significant epistatic interaction accounted for 46% of the total phenotypic variation. Heterozygosity per se was not predictive of phenotypic performance.     

A wheat genomic DNA fragment reduces pollen transmission of maize transgenes by reducing pollen viability

A genomic DNA fragment from wheat carrying the Glu-1Dx5 gene has been shown to exhibit reduced pollen transmission in transgenic maize. To localize the region of the DNA fragment responsible for this reduced pollen transmission, we produced transgenic maize plants in which the wheat genomic DNA proximal to the 1Dx5 coding sequence was replaced with the maize 27 kDa gamma-zein promoter. Like the wheat promoter-driven Glu-1Dx5 transgene, this zein promoter-driven transgene functioned to produce 1Dx5 in maize endosperm. However, with the zein promoter-driven transgene, pollen transmission of the transgene loci was normal in most self- and cross-pollinations. We concluded that the wheat genomic DNA proximal to the wheat 1Dx5 coding sequence was required for reduced pollen transmission of the transgene in maize. In two of four transformation events of the wheat promoter-driven construct examined, pollen exhibited two morphological classes. In one class, pollen was normal in morphology and displayed average viability, and in the second, pollen was reduced in size and did not germinate on artificial media. DNA from the transgene was detectable in mature pollen from plants with reduced pollen transmission of transgene loci. To explain these observations, we hypothesize that elements within the transgene construct interfere with pollen development. We demonstrated that the wheat genomic DNA fragment can be used to control pollen transmission of an herbicide resistance transgene genetically linked to it. The wheat genomic DNA fragment may contain elements that are useful for controlling pollen transmission of transgene loci in commercial maize grain and seed production.     

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

Momordica charantia is a monoecious plant of the Cucurbitaceae family that has both male and female unisexual flowers. Its unique gynoecious line, OHB61-5, is essential as a maternal parent in the production of F₁ cultivars. To identify the DNA markers for this gynoecy, a RAD-seq (restriction-associated DNA tag sequencing) analysis was employed to reveal genome-wide DNA polymorphisms and to genotype the F₂ progeny from a cross between OHB61-5 and a monoecious line. Based on a RAD-seq analysis of F₂ individuals, a linkage map was constructed using 552 co-dominant markers. In addition, after analyzing the pooled genomic DNA from monoecious or gynoecious F₂ plants, several SNP loci that are genetically linked to gynoecy were identified. GTFL-1, the closest SNP locus to the putative gynoecious locus, was converted to a conventional DNA marker using invader assay technology, which is applicable to the marker-assisted selection of gynoecy in M. charantia breeding.     

Molecular evidence for post-domestication selection in the <Emphasis Type="Italic">Waxy</Emphasis> gene of Chinese waxy maize

Waxy maize was first reported in China in 1909 and is mainly used in food production in Asia. The evidence for strong domestication selection in the Waxy locus of rice and a selective sweep around its genomic region make us to wonder whether there has been similar selection in Waxy in glutinous maize. To address this issue, DNA sequences of Waxy, three flanking genes and an unlinked gene (Adh1) of 30 accessions sampled from Chinese waxy maize accessions, including representative landraces and inbred lines, were determined in this study. Sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed in the Waxy locus in Chinese waxy maize but not in nonglutinous maize; comparison with the unlinked gene confirmed that this pattern was different to Waxy. Sequence analysis across a 143 kb genomic segment centered on the Waxy locus revealed patterns consistent with a selective sweep in the upstream region of Waxy. The selective sweep detected based on current limited genomic sequences exceeded over 50 kb, indicating strong selection in this or a bigger region. However, No sweep effect was detected in the repetitive downstream region of Waxy. Phylogenetic analysis indicated that Chinese waxy maize was domesticated from the cultivated flint maize (Zea mays ssp. mays) that was introduced from the new world. At least two independent deletions in exon 7 (30 bp) and 10 (15 bp) were identified in the Chinese accessions respectively. These findings demonstrate a similar pattern of domestication selection in the Waxy genomic region in both glutinous maize and rice, suggesting that this pattern in the rise of glutinous phenotype is likely in other cereal crops.