On the origin of six-rowed barley with brittle rachis, agriocrithon [Hordeum vulgare ssp. vulgare f. agriocrithon (Aberg) Bowd.], based on a DNA marker closely linked to the vrs1 (six-row gene) locus

The origin of six-rowed cultivated barley has been revealed to be more complex since the discovery of agriocrithon, a six-rowed barley with brittle rachis. The present study investigates whether such six-rowed brittle barley is wild or hybrid in nature, by analyzing genetic diversity at the cMWG699 marker locus, which is closely linked to the vrs1 (six-row gene) locus. DNA sequence analysis for 42 accessions showed only three types in six-rowed brittle barleys; in contrast, nine sequence types were found in ten wild barleys, ssp. spontaneum, in our previous study. Nucleotide diversities for the six-rowed brittle barley were 2.8–4.5 times lower than that for the ssp. spontaneum at this marker locus. The three sequence types found in the six-rowed brittle barley also appeared in the six-rowed cultivated barley. A cross-allelism test confirmed that the six-rowed character of the six-rowed brittle barley was controlled by the vrs1 locus. The nucleotide diversity and genealogy demonstrated that f. agriocrithon does not have the same level of diversity as found in wild barley, ssp. spontaneum. Consequently, f. agriocrithon does not appear to represent genuinely wild populations, but more probably originated from hybridization between ssp. spontaneum and six-rowed cultivated barley.     

High-density AFLP map of nonbrittle rachis 1 (<Emphasis Type="Italic">btr1</Emphasis>) and 2 (<Emphasis Type="Italic">btr2</Emphasis>) genes in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

Wild relatives of barley disperse their seeds at maturity by means of their brittle rachis. In cultivated barley, brittleness of the rachis was lost during domestication. Nonbrittle rachis of occidental barley lines is controlled by a single gene (btr1) on chromosome 3H. However, nonbrittle rachis of oriental barley lines is controlled by a major gene (btr2) on chromosome 3H and two quantitative trait loci on chromosomes 5HL and 7H. This result suggests multiple mutations of the genes involved in the formation of brittle rachis in oriental lines. The btr1 and btr2 loci did not recombine in the mapping population analyzed. This result agrees with the theory of tight linkage between the two loci. A high-density amplified fragment-length polymorphism (AFLP) map of the btr1/btr2 region was constructed, providing an average density of 0.08 cM/locus. A phylogenetic tree based on the AFLPs showed clear separation of occidental and oriental barley lines. Thus, barley consists of at least two lineages as far as revealed by molecular markers linked to nonbrittle rachis genes.Electronic Supplementary Material Supplementary material is available for this article at An erratum to this article can be found at     

A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley

BACKGROUND AND AIMS: Barley (Hordeum vulgare ssp. vulgare) cultivation started between 9500 and 8400 years ago, and was a major part of ancient agriculture in the Near East. The brittle rachis is a critical trait in the domestication process. METHODS: A DNA sequence closely linked to the brittle rachis complex was amplified and resequenced in a collection of cultivated barleys, wild barleys (H. vulgare ssp. spontaneum) and weedy brittle rachis varieties (H. vulgare ssp. vulgare var. agriocrithon). The sequence was used to construct a phylogenetic tree. KEY RESULTS: The phylogeny separated the W- (btr1-carrying) from the E- (btr2-carrying) cultivars. The wild barleys had a high sequence diversity and were distributed throughout the W- and E-clades. Some of the Tibetan var. agriocrithon lines were closely related to the E-type and others to the W-type cultivated barleys, but an Israeli var. agriocrithon line has a complex origin. CONCLUSIONS: The results are consistent with a diphyletic origin of barley. The W- and E-type cultivars are assumed to have evolved from previously diverged wild barley via independent mutations at Btr1 and Btr2.     

Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.)

The mature spike rachis of wild emmer [Triticum turgidum L. ssp. dicoccoides (Körn. ex Asch. and Graebner) Thell.] disarticulates spontaneously between each spikelet leading to the dispersion of wedge-type diaspores. By contrast, the spike rachis of domesticated emmer (Triticum turgidum L. ssp. turgidum) fails to disarticulate and remains intact until it is harvested. This major distinguishing feature between wild and domesticated emmer is controlled by two major genes, brittle rachis 2 (Br-A2) and brittle rachis 3 (Br-A3) on the short arms of chromosomes 3A and 3B, respectively. Because of their biological and agricultural importance, a map-based analysis of these genes was undertaken. Using two recombinant inbred chromosome line (RICL) populations, Br-A2, on chromosome 3A, was localized to a ~11-cM region between Xgwm2 and a cluster of linked loci (Xgwm666.1, Xbarc19, Xcfa2164, Xbarc356, and Xgwm674), whereas Br-A3, on chromosome 3B, was localized to a ~24-cM interval between Xbarc218 and Xwmc777. Comparative mapping analyses suggested that both Br-A2 and Br-A3 were present in homoeologous regions on chromosomes 3A and 3B, respectively. Furthermore, Br-A2 and Br-A3 from wheat and Btr1/Btr2 on chromosome 3H of barley (Hordeum vulgare L.) also were homoeologous suggesting that the location of major determinants of the brittle rachis trait in these species has been conserved. On the other hand, brittle rachis loci of wheat and barley, and a shattering locus on rice chromosome 1 did not appear to be orthologous. Linkage and deletion-based bin mapping comparisons suggested that Br-A2 and Br-A3 may reside in chromosomal areas where the estimated frequency of recombination was ~ 4.3 Mb/cM. These estimates indicated that the cloning of Br-A2 and Br-A3 using map-based methods would be extremely challenging.     

Molecular marker assisted genetic analysis of head shattering in six-rowed barley

Head shattering in barley (Hordeum vulgare L.) has two forms; brittle rachis and weak rachis. Brittle rachis is not observed in cultivated barley since all cultivars carry non-brittle alleles at one of the two complementary brittle rachis loci (Btr1;Btr2). Weak rachis causes head shattering in barley cultivars and may be confused with brittle rachis. Brittle rachis has been mapped to the chromosome 3 (3H) short arm while map position(s) of the weak rachis is unknown. Two major and a putative minor QTL for head shattering were mapped using the Steptoe × Morex doubled haploid line population. The largest QTL, designated Hst-3, located on the chromosome 3 (3H) centromeric region, is associated with a major yield QTL. The Steptoe Hst-3 region, when transferred into Morex, resulted in a substantial decrease in head shattering. High-resolution mapping of Hst-3 was achieved using isogenic lines. Brittle rachis was mapped with molecular markers and shown to be located in a different position from that of Hst-3. The second major QTL, designated Hst-2 S, is located on chromosome 2 S. This locus is associated with an environmentally sensitive yield QTL.     

Molecular mapping of the intermedium spike-c ( int-c) and non-brittle rachis 1 ( btr1) loci in barley ( Hordeum vulgare L.)

Lateral spikelet fertility and a non-brittle rachis are key characters in studying the evolution of barley. The fertility of lateral spikelets is controlled predominantly by the alleles at the vrs1 locus on chromosome 2HL and is modified by the alleles at the int-c locus on chromosome 4HS. The non-brittle rachis is controlled by alleles at two tightly linked loci, btr1 and btr2, on chromosome 3HS. This paper presents the integration of the int-c and btr1 loci in molecular linkage maps of barley. The int-c locus was mapped to the end of chromosome 4HS, 8.2 cM distal from the MWG2033 locus. The analysis was followed by a composite interval mapping of quantitative trait loci, which verified the position of the int-c locus. Linkage analysis using recombinant inbred lines showed that the btr1 locus is flanked between two AFLP loci, e14m27.4.1 and e15m19.7, with map distances of 3.1 cM and 4.2 cM, respectively. The molecular markers will expedite further high-density mapping of the int-c and btr1 loci.     

A DNA marker closely linked to the <Emphasis Type="Italic">vrs1</Emphasis> locus (row-type gene) indicates multiple origins of six-rowed cultivated barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

The origin of six-rowed cultivated barley was studied using a DNA marker cMWG699 closely linked to the vrs1 locus. Restriction patterns of the PCR-amplified product of the cMWG699 locus were examined in 280 cultivated (Hordeum vulgare ssp. vulgare) and 183 wild (H. vulgare ssp. spontaneum) barleys. Nucleotide sequences of the PCR products were also examined in selected accessions. Six-rowed cultivated barleys were divided into two distinct groups, types I and II. Type I six-rowed cultivated barley was distributed widely while type II six-rowed cultivated barley was found only in the Mediterranean region. The type I sequence was also found in a wild barley accession from Turkmenistan whereas the type II sequence was also found in a two-rowed cultivated barley from North Africa and a wild barley from Morocco. These results suggested that the six-rowed type I and II barleys were derived from two-rowed type I and II barleys, respectively, by independent mutations at the vrs1 locus. Received: 3 November 2000 / Accepted: 17 April 2001     

Roles of BdUNICULME4 and BdLAXATUM‐A in the non‐domesticated grass Brachypodium distachyon

In cultivated grasses, tillering, spike architecture and seed shattering represent major agronomical traits. In barley, maize and rice, the NOOT‐BOP‐COCH‐LIKE (NBCL) genes play important roles in development, especially in ligule development, tillering and flower identity. However, compared with dicots, the role of grass NBCL genes is underinvestigated. To better understand the role of grass NBCLs and to overcome any effects of domestication that might conceal their original functions, we studied TILLING nbcl mutants in the non‐domesticated grass Brachypodium distachyon. In B. distachyon, the NBCL genes BdUNICULME4 (CUL4) and BdLAXATUM‐A (LAXA) are orthologous, respectively, to the barley HvUniculme4 and HvLaxatum‐a, to the maize Zmtassels replace upper ears1 and Zmtassels replace upper ears2 and to the rice OsBLADE‐ON‐PETIOLE1 and OsBLADE‐ON‐PETIOLE2/3. In B. distachyon, our reverse genetics study shows that CUL4 is not essential for the establishment of the blade–sheath boundary but is necessary for the development of the ligule and auricles. We report that CUL4 also exerts a positive role in tillering and a negative role in spikelet meristem activity. On the other hand, we demonstrate that LAXA plays a negative role in tillering, positively participates in spikelet development and contributes to the control of floral organ number and identity. In this work, we functionally characterized two new NBCL genes in a context of non‐domesticated grass and highlighted original roles for grass NBCL genes that are related to important agronomical traits.     

The highly divergent Jekyll genes,required for sexual reproduction,are lineage specific for the related grass tribes Triticeae and Bromeae

Phylogenetically related groups of species contain lineage‐specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the Jekyll gene, required for sexual reproduction, exists in two much diverged allelic variants, Jek1 and Jek3. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. Jek3 has a similar expression as Jek1 and complements the Jek1 function in Jek1‐deficient plants. Jek1 and Jek3 allelic variants were almost equally distributed in a collection of 485 wild and domesticated barley accessions. All domesticated barleys harboring the Jek1 allele belong to single haplotype J1‐H1 indicating a genetic bottleneck during domestication. Domesticated barleys harboring the Jek3 allele consisted of three haplotypes. Jekyll‐like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non‐invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the Jekyll function. The emergence of Jekyll suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the Jekyll genes as lineage‐specific.     

Polymorphism pattern at a miniature inverted‐repeat transposable element locus downstream of the domestication gene Teosinte‐branched1 in wild and domesticated pearl millet

Unravelling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits is central to this issue. Pearl millet, a domesticated grass mostly found in semi‐arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary branches in comparison with the wild phenotype. Two recent studies have shown that the orthologue of the maize gene Teosinte‐Branched1 in pearl millet (PgTb1) was probably involved in branching evolution during domestication and that a miniature inverted‐repeat transposable element (MITE) of the Tuareg family was inserted in the 3′ untranslated region of PgTb1. For a set of 35 wild and domesticated populations, we compared the polymorphism patterns at this MITE and at microsatellite loci. The Tuareg insertion was nearly absent in the wild populations, whereas a strong longitudinal frequency cline was observed in the domesticated populations. The geographical pattern revealed by neutral microsatellite loci clearly demonstrated that isolation by distance does not account for the existence of this cline. However, comparison of population differentiation at the microsatellite and the MITE loci and analyses of the nucleotide polymorphism pattern in the downstream region of PgTb1 did not show evidence that the cline at the MITE locus has been shaped by selection, suggesting the implication of a neutral process. Alternative hypotheses are discussed.     

Resequencing the<Emphasis Type="Italic">Vrs1</Emphasis> gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike

Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and has been often associated to phenotypic traits beyond spike type. Comprehensive re-sequencing Vrs1 revealed three two-rowed alleles (Vrs1.b2; Vrs1.b3; Vrs1.t1) and four six-rowed (vrs1.a1; vrs1.a2; vrs1.a3; vrs1.a4) in the natural population. However, the current knowledge about Vrs1 alleles and its distribution among Spanish barley subpopulations is still underexploited. We analyzed the gene in a panel of 215 genotypes, made of Spanish landraces and European cultivars. Among 143 six-rowed accessions, 57 had the vrs1.a1 allele, 83 were vrs1.a2, and three showed the vrs1.a3 allele. Vrs1.b3 was found in most two-rowed accessions, and a new allele was observed in 7 out of 50 two-rowed Spanish landraces. This allele, named Vrs1.b5, contains a ‘T’ insertion in exon 2, originally proposed as the causal mutation giving rise to the six-row vrs1.a2 allele, but has an additional upstream deletion that results in the change of 15 amino acids and a potentially functional protein. We conclude that eight Vrs1 alleles (Vrs1.b2, Vrs1.b3, Vrs1.b5, Vrs1.t1, vrs1.a1, vrs1.a2, vrs1.a3, vrs1.a4) discriminate two and six-rowed barleys. The markers described will be useful for DUS identification, plant breeders, and other crop scientists.     

Diversity of Rice yellow mottle virus in Benin and Togo and Screening for Resistant Accessions

Surveys were conducted in rice fields in Benin, Cote d'Ivoire, Mali, Nigeria, Togo and Niger to assess the importance of Rice yellow mottle virus (RYMV). Diseased leaf samples were collected. In Togo, surveys were made mainly in the southern part of the country, and in Benin, all areas where rice is grown were covered. Leaf samples were serologically confirmed by ACP ELISA as bearing RYMV, propagated and all conserved. One hundred and forty‐eight (148) Beninese and 27 Togolese strains were serotyped. They were also phenotyped on three susceptible accessions including IR 64, four resistant lines with known alleles on RYMV 1 gene namely TOG 5681 (rymv 1‐3), TOG 5672 (rymv 1‐4 and RYMV 2), TOG 5674 (rymv 1.5) and Gigante (rymv 1‐2). RYMV spots with 9–100% incidences were identified. Serotyping by triple antibody sandwich (TAS) ELISA indicated that two main groups S1 and S2 coexisted in Benin with S1 being prevalent. In Togo, 26 strains were S1 and only one was S2. Phenotyping of the 148 Beninese and 27 Togolese indicated that they all attacked the three susceptible accessions, while TOG 5681 (rymv 1‐3), TOG 5672 (rymv 1‐4 and RYMV 2), TOG 5674 (rymv 1‐5) and Gigante (rymv 1‐2) remained symptomless. The use of the genes/alleles above in these countries against the disease is discussed. Three representative Beninese strains were selected to screen 48 accessions for disease resistance. Nine accessions were as susceptible as IR 64 to all strains while six (NERICA 9, NERICA 12, NERICA 13, TOG 7291, WAB56‐50, CG 14 and Moroberekan) were very resistant. Susceptibility of the six ARICA and resistance of some NERICA lines could be explained by the fact that one or both parental lines were, respectively, susceptible or resistant to the strains.     

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ‘domestication syndrome’. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non‐orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ‘classic’ domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non‐overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.     

Construction and comparison of three reference‐quality genome assemblies for soybean

We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.     

A VIGS screen identifies immunity in the Arabidopsis Pla‐1 accession to viruses in two different genera of the Geminiviridae

Geminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus‐resistant genes that derive from alterations in essential host factors. We used a virus‐induced gene silencing (VIGS) vector derived from the geminivirus Cabbage leaf curl virus (CaLCuV) to assess natural variation in virus–host interactions in 190 Arabidopsis accessions. Silencing of CH‐42, encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance. There was a wide range in symptom severity and extent of silencing in different accessions, but two correlations could be made. Lines with severe symptoms uniformly lacked extensive VIGS, and lines that showed attenuated symptoms over time (recovery) showed a concomitant increase in the extent of VIGS. One accession, Pla‐1, lacked both symptoms and silencing, and was immune to wild‐type infectious clones corresponding to CaLCuV or Beet curly top virus (BCTV), which are classified in different genera in the Geminiviridae. It also showed resistance to the agronomically important Tomato yellow leaf curl virus (TYLCV). Quantitative trait locus mapping of a Pla‐1 X Col‐0 F₂ population was used to detect a major peak on chromosome 1, which is designated gip‐1 (geminivirus immunity Pla‐1‐1). The recessive nature of resistance to CaLCuV and the lack of obvious candidate genes near the gip‐1 locus suggest that a novel resistance gene(s) confers immunity.     

High intraspecific diversity of Restorer‐of‐fertility‐like genes in barley

Nuclear restorer of fertility (Rf) genes suppress the effects of mitochondrial genes causing cytoplasmic male sterility (CMS), a condition in which plants fail to produce viable pollen. Rf genes, many of which encode RNA‐binding pentatricopeptide repeat (PPR) proteins, are applied in hybrid breeding to overcome CMS used to block self‐pollination of the seed parent. Here, we characterise the repertoire of restorer‐of‐fertility‐like (RFL) PPR genes in barley (Hordeum vulgare). We found 26 RFL genes in the reference genome (‘Morex’) and an additional 51 putative orthogroups (POGs) in a re‐sequencing data set from 262 barley genotypes and landraces. Whereas the sequences of some POGs are highly conserved across hundreds of barley accessions, the sequences of others are much more variable. High sequence variation strongly correlates with genomic location – the most variable genes are found in a cluster on chromosome 1H. A much higher likelihood of diversifying selection was found for genes within this cluster than for genes present as singlets. This work includes a comprehensive analysis of the patterns of intraspecific variation of RFL genes. The RFL sequences characterised in this study will be useful for the development of new markers for fertility restoration loci.     

Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones

Miscanthus × giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type‐specimen. A subset of accessions was also evaluated by restriction‐site associated DNA sequencing (RAD‐seq). In addition, we assessed the potential of new crosses to increase Mxg genetic diversity by comparing eight new triploid Mxg progeny grown from seed, along with samples of the parental species M. sacchariflorus and M. sinensis. Estimates of genotyping error rates were essential for distinguishing between experimental error and true genotypic differences among accessions. Given differences in estimated error rates and costs per marker for SSRs and RAD‐seq, the former is currently more cost‐effective for determining if two accessions are genetically identical. We concluded that all of the Mxg legacy cultivars were derived via vegetative propagation from a single genet. In contrast with the Mxg legacy cultivars, genetic similarity to the type‐specimen of eight new triploid Mxg progeny ranged from 0.46 to 0.56. Though genetic diversity among the Mxg legacy cultivars is critically low, new crosses can provide much‐needed variation to growers.     

Identification structure of the mating‐type locus and distribution of Kabatiella zeae in China

The 51 isolates, the causing agents of maize eyespot, were identified as Kabatiella zeae with morphological and molecular methods. The structure of the MAT locus in K. zeae JLMHK‐9 strain contains MAT1‐1 and MAT1‐2 genes which are transcribed in opposite directions, DNA lyase gene (APN2) which is adjacent to the 3′ flanking region of MAT1‐2‐1 gene and a pleckstrin homology domain (PH) which is adjacent to the 3′ flanking region of MAT1‐1‐1 gene. The specific primers are used to identify the mating types of K. zeae isolates collected from six provinces in China, and our findings speculate that K. zeae is a homothallic species.