The domestication of crop plants has often involved an increase in apical dominance (the concentration of resources in the main stem of the plant and a corresponding suppression of axillary branches). A striking example of this phenomenon is seen in maize (Zea mays spp. mays), which exhibits a profound increase in apical dominance compared with its probable wild ancestor, teosinte (Zea mays ssp. parviglumis). Previous research has identified the teosinte branched1 (tb1) gene as a major contributor to this evolutionary change in maize. We have cloned tb1 by transposon tagging and show here that it encodes a protein with homology to the cycloidea gene of snapdragon. The pattern of tb1 expression and the morphology of tb1 mutant plants suggest that tb1 acts both to repress the growth of axillary organs and to enable the formation of female inflorescences. The maize allele of tb1 is expressed at twice the level of the teosinte allele, suggesting that gene regulatory changes underlie the evolutionary divergence of maize from teosinte.

The domestication of all major crop plants occurred during a brief period in human history about 10,000 years ago. During this time, ancient agriculturalists selected seed of preferred forms and culled out seed of undesirable types to produce each subsequent generation. Consequently, favoured alleles at genes controlling traits of interest increased in frequency, ultimately reaching fixation. When selection is strong, domestication has the potential to drastically reduce genetic diversity in a crop. To understand the impact of selection during maize domestication, we examined nucleotide polymorphism in teosinte branched1, a gene involved in maize evolution. Here we show that the effects of selection were limited to the gene's regulatory region and cannot be detected in the protein-coding region. Although selection was apparently strong, high rates of recombination and a prolonged domestication period probably limited its effects. Our results help to explain why maize is such a variable crop. They also suggest that maize domestication required hundreds of years, and confirm previous evidence that maize was domesticated from Balsas teosinte of southwestern Mexico.

Genes controlling the dramatic morphological differences between maize and its presumed progenitor (teosinte) were investigated in a maize-teosinte F2 population through the use of molecular markers. Results indicate that the key traits differentiating maize and teosinte are each under multigenic control, although for some traits, such as the number of ranks of cupules, the data are consistent with a mode of inheritance that would involve a single major locus plus several modifiers. For other traits, such as the presence/absence of the pedicellate spikelet, the data indicate multigenic inheritance with no single locus having a dramatically larger effect than the others. Results also indicate that the tunicate locus (Tu) had no major role in the origin of maize, despite previous opinion that it was involved. The major loci affecting the morphological differences between maize and teosinte are located on the first four chromosomes. The data suggest that the differences between teosinte and maize involve, in part, developmental modifications that enable (i) primary lateral inflorescences, which are programmed to develop into tassels (male) in teosinte, to become ears (female) in maize, and (ii) the expression of male secondary sex traits on a female background in maize. Similar changes were likely involved in the origin of maize.

Teosinte, the probable progenitor of maize, has kernels that are encased in hardened fruitcases, which interfere with the use of the kernels as food. Although the components of the fruitcase are present in maize, their development is disrupted so that the kernels are not encased as in teosinte but exposed on the ear. The change from encased to exposed kernels represents a key step in maize evolution. The locus that largely controls this morphological difference between maize and teosinte, teosinte glume architecture 1, is described and genetically mapped.

All 10 chromosomes of maize (Zea mays, 2n ϭ 2x ϭ 20) were recovered as single additions to the haploid complement of oat (Avena sativa, 2n ϭ 6x ϭ 42) among F 1 plants generated from crosses involving three different lines of maize to eight different lines of oat. In vitro rescue culture of more than 4,300 immature F 1 embryos resulted in a germination frequency of 11% with recovery of 379 F 1 plantlets (8.7%) of moderately vigorous growth. Some F 1 plants were sectored with distinct chromosome constitutions among tillers of the same plant and also between root and shoot cells. Meiotic restitution facilitated development of un-reduced gametes in the F 1. Self-pollination of these partially fertile F 1 plants resulted in disomic additions (2n ϭ 6x ϩ 2 ϭ 44) for maize chromosomes 1, 2, 3, 4, 6, 7, and 9. Maize chromosome 8 was recovered as a monosomic addition (2n ϭ 6x ϩ 1 ϭ 43). Monosomic additions for maize chromosomes 5 and 10 to a haploid complement of oat (n ϭ 3x ϩ 1 ϭ 22) were recovered several times among the F 1 plants. Although partially fertile, these chromosome 5 and 10 addition plants have not yet transmitted the added maize chromosome to F 2 offspring. We discuss the development and general utility of this set of oat-maize addition lines as a novel tool for maize genomics and genetics.

Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.

Summary Soybean cyst nematode ( SCN ) is the most devastating plant‐parasitic nematode. Most commercial soybean varieties with SCN resistance are derived from PI 88788. Resistance derived from PI 88788 is breaking down due to narrow genetic background and SCN population shift. PI 88788 requires mainly the rhg1‐b locus, while ‘Peking’ requires rhg1‐a and Rhg4 for SCN resistance. In the present study, whole genome re‐sequencing of 106 soybean lines was used to define the Rhg haplotypes and investigate their responses to the SCN HG ‐Types. The analysis showed a comprehensive profile of SNP s and copy number variations ( CNV ) at these loci. CNV of rhg1 (Gm SNAP 18) only contributed towards resistance in lines derived from PI 88788 and ‘Cloud’. At least 5.6 copies of the PI 88788‐type rhg1 were required to confer SCN resistance, regardless of the Rhg4 ( Gm SHMT 08 ) haplotype. However, when the Gm SNAP 18 copies dropped below 5.6, a ‘Peking’‐type Gm SHMT 08 haplotype was required to ensure SCN resistance. This points to a novel mechanism of epistasis between Gm SNAP 18 and Gm SHMT 08 involving minimum requirements for copy number. The presence of more Rhg4 copies confers resistance to multiple SCN races. Moreover, transcript abundance of the Gm SHMT 08 in root tissue correlates with more copies of the Rhg4 locus, reinforcing SCN resistance. Finally, haplotype analysis of the Gm SHMT 08 and Gm SNAP 18 promoters inferred additional levels of the resistance mechanism. This is the first report revealing the genetic basis of broad‐based resistance to SCN and providing new insight into epistasis, haplotype‐compatibility, CNV , promoter variation and its impact on broad‐based disease resistance in plants.

SummaryProcessing of double‐stranded RNA precursors into small RNAs is an essential regulator of gene expression in plant development and stress response. Small RNA processing requires the combined activity of a functionally diverse group of molecular components. However, in most of the plant species, there are insufficient mutant resources to functionally characterize each encoding gene. Here, mutations in loci encoding protein machinery involved in small RNA processing in soya bean and Medicago truncatula were generated using the CRISPR/Cas9 and TAL‐effector nuclease (TALEN) mutagenesis platforms. An efficient CRISPR/Cas9 reagent was used to create a bi‐allelic double mutant for the two soya bean paralogous Double‐stranded RNA‐binding2 (GmDrb2a and GmDrb2b) genes. These mutations, along with a CRISPR/Cas9‐generated mutation of the M. truncatula Hua enhancer1 (MtHen1) gene, were determined to be germ‐line transmissible. Furthermore, TALENs were used to generate a mutation within the soya bean Dicer‐like2 gene. CRISPR/Cas9 mutagenesis of the soya bean Dicer‐like3 gene and the GmHen1a gene was observed in the T0 generation, but these mutations failed to transmit to the T1 generation. The irregular transmission of induced mutations and the corresponding transgenes was investigated by whole‐genome sequencing to reveal a spectrum of non‐germ‐line‐targeted mutations and multiple transgene insertion events. Finally, a suite of combinatorial mutant plants were generated by combining the previously reported Gmdcl1a, Gmdcl1b and Gmdcl4b mutants with the Gmdrb2ab double mutant. Altogether, this study demonstrates the synergistic use of different genome engineering platforms to generate a collection of useful mutant plant lines for future study of small RNA processing in legume crops.