Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials

A common difficulty in mapping quantitative trait loci (QTLs) is that QTL effects may show environment specificity and thus differ across environments. Furthermore, quantitative traits are likely to be influenced by multiple QTLs or genes having different effect sizes. There is currently a need for efficient mapping strategies to account for both multiple QTLs and marker-by-environment interactions. Thus, the objective of our study was to develop a Bayesian multi-locus multi-environmental method of QTL analysis. This strategy is compared to (1) Bayesian multi-locus mapping, where each environment is analysed separately, (2) Restricted Maximum Likelihood (REML) single-locus method using a mixed hierarchical model, and (3) REML forward selection applying a mixed hierarchical model. For this study, we used data on multi-environmental field trials of 301 BC2DH lines derived from a cross between the spring barley elite cultivar Scarlett and the wild donor ISR42-8 from Israel. The lines were genotyped by 98 SSR markers and measured for the agronomic traits “ears per m²,” “days until heading,” “plant height,” “thousand grain weight,” and “grain yield”. Additionally, a simulation study was performed to verify the QTL results obtained in the spring barley population. In general, the results of Bayesian QTL mapping are in accordance with REML methods. In this study, Bayesian multi-locus multi-environmental analysis is a valuable method that is particularly suitable if lines are cultivated in multi-environmental field trials

Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs

Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or ‘kinship’ information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of marker–trait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well

High-resolution genetic mapping and physical map construction for the fertility restorer Rfm1 locus in barley

KEY MESSAGE: High-resolution genetic linkage mapping and BAC physical mapping narrowed the fertility restorer locus Rfm1 in barley to a sub-centimorgan genetic interval and a 208-kb physical interval. Rfm1 restores the fertility of msm1 and msm2 male-sterile cytoplasms in barley. The fertility restoration gene is located on the short arm of chromosome 6H (6HS), and we pursued a positional cloning of this gene. Starting from a previous result that has delimited Rfm1 within a 10.8 cM region on 6HS, we developed novel CAPS and SSR markers tightly linked to the gene in barley using the sequence information from the syntenic region of rice and barley genome assemblies. Next, we performed fine mapping of the Rfm1 locus. To isolate recombinants, we surveyed 3,638 F2 plants derived from a cross between the CMS strain and the Rf strain with adjacent markers (NAS2090 and NAS1080). This analysis identified 175 recombinant plants from the F2 population to build a high-resolution map with nine markers tightly linked to the Rfm1 locus. Rfm1 was located within the 0.14 cM region delimited by two markers (NAS9113 and NAS9200). Using these flanking markers as well as marker cosegregating with Rfm1 (NAS9133), we screened the BAC libraries of the cultivar Morex, an rfm1 carrier. We isolated 11 BAC clones and constructed a BAC physical map using their fingerprints. Finally, we delimited the Rfm1 locus encompassing the rfm1 allele on a 208-kb contig composed of three minimally overlapping BAC clones. This precise localization of the Rfm1 locus in the barley genome is expected to greatly accelerate the future map-based cloning of the Rfm1 gene by sequence analysis and its genetic transformation for the complementation of cytoplasmic male-sterile plants

Genetic targeting of candidate genes for drought sensitive gene eibi1 of wild barley (Hordeum spontaneum)

Drought stress is one of the most severe abiotic stresses that cause the loss of crop yield. The cuticle protects the leaf from dehydration in the face of drought stress. The barley cuticle mutant eibi1 is highly drought sensitive. Here, we describe the fine-scale genetic mapping of the eibi1 locus, based on a cv. Morex × eibi1 F population of 1,682 individuals. Barley-rice synteny was exploited to identify markers for mapping and to identify candidate genes for Eibi1. The target segment of chromosome 3H is perfectly collinear with the equivalent region on rice chromosome 1. Marker enrichment delimited eibi1 to a 0.11 cM barley region defined by the interval BI958842-Os01g0176800*, which in rice consists of a 112.8 kbp segment. Gene prediction revealed that this rice segment harbours 16 genes. Of them, five (Os01g0177100, Os01g0177200, Os01g0177900, Os01g0178200 and Os01g0178400) were proposed as candidate genes of Eibi1.

An alternative mechanism for cleistogamy in barley

Cleistogamy in barley is genetically determined by the presence of the recessive allele cly1, but the dominant allele at the linked locus Cly2 is epistatic over cly1. Although the molecular basis for cly1 action is well understood, that of Cly2 is not. Here we show that anther non-extrusion can occur not just when the lodicules fail to expand adequately (a trait which is fully determined by the allelic state at the cly1 locus), but by the premature timing of anthesis before the spike has emerged from the boot. The transcription of HvAP2 at cly1 is unaffected by the timing of anthesis. Where this occurs prematurely, by the time that the spike has emerged from the boot, the lodicules have already become shrunken and have lost the capacity to push the lemma and palea apart. Premature anthesis appears to be governed by a dominant gene, probably Cly2. Of the three phases of development of a non-cleistogamous barley floret (spike emergence from the boot, floret gaping induced by lodicule expansion and anther extrusion), genetic variation is available regarding at least the former two

Evolution of the grain dispersal system in barley

Published: July 30, 2015About 12,000 years ago in the Near East, humans began the transition from hunter-gathering to agriculture-based societies. Barley was a founder crop in this process, and the most important steps in its domestication were mutations in two adjacent, dominant, and complementary genes, through which grains were retained on the inflorescence at maturity, enabling effective harvesting. Independent recessive mutations in each of these genes caused cell wall thickening in a highly specific grain "disarticulation zone," converting the brittle floral axis (the rachis) of the wild-type into a tough, non-brittle form that promoted grain retention. By tracing the evolutionary history of allelic variation in both genes, we conclude that spatially and temporally independent selections of germplasm with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies.Mohammad Pourkheirandish, Goetz Hensel, Benjamin Kilian, Natesan Senthil, Guoxiong Chen, Mohammad Sameri, Perumal Azhaguvel, Shun Sakuma, Sidram Dhanagond, Rajiv Sharma, Martin Mascher, Axel Himmelbach, Sven Gottwald, Sudha K. Nair, Akemi Tagiri, Fumiko Yukuhiro, Yoshiaki Nagamura, Hiroyuki Kanamori, Takashi Matsumoto, George Willcox, Christopher P. Middleton, Thomas Wicker, Alexander Walther, Robbie Waugh, Geoffrey B. Fincher, Nils Stein, Jochen Kumlehn, Kazuhiro Sato, and Takao Komatsud

Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage

The cleistogamous flower sheds its pollen before opening, forcing plants with this habit to be almost entirely autogamous. Cleistogamy also provides a means of escape from cereal head blight infection and minimizes pollen-mediated gene flow. The lodicule in cleistogamous barley is atrophied. We have isolated cleistogamy 1 (Cly1) by positional cloning and show that it encodes a transcription factor containing two AP2 domains and a putative microRNA miR172 targeting site, which is an ortholog of Arabidopsis thaliana AP2. The expression of Cly1 was concentrated within the lodicule primordia. We established a perfect association between a synonymous nucleotide substitution at the miR172 targeting site and cleistogamy. Cleavage of mRNA directed by miR172 was detectable only in a noncleistogamous background. We conclude that the miR172-derived down-regulation of Cly1 promotes the development of the lodicules, thereby ensuring noncleistogamy, although the single nucleotide change at the miR172 targeting site results in the failure of the lodicules to develop properly, producing the cleistogamous phenotype