SELF-INCOMPATIBILITY IN RYE

Characterization and practical use of self-compatibility in outcrossing grass species

BACKGROUND

Self-incompatibility (SI) systems prevent self-fertilization in several species of Poaceae, many of which are economically important forage, bioenergy and turf grasses. Self-incompatibility ensures cross-pollination and genetic diversity but restricts the ability to fix useful genetic variation. In most inbred crops it is possible to develop high-performing homozygous parental lines by self-pollination, which then enables the creation of F1 hybrid varieties with higher performance, a phenomenon known as heterosis. The inability to fully exploit heterosis in outcrossing grasses is partially responsible for lower levels of improvement in breeding programmes compared with inbred crops. However, SI can be overcome in forage grasses to create self-compatible populations. This is generating interest in understanding the genetical basis of self-compatibility (SC), its significance for reproductive strategies and its exploitation for crop improvement, especially in the context of F1 hybrid breeding.

SCOPE

We review the literature on SI and SC in outcrossing grass species. We review the currently available genomic tools and approaches used to discover and characterize novel SC sources. We discuss opportunities barely explored for outcrossing grasses that SC facilitates. Specifically, we discuss strategies for wide SC introgression in the context of the Lolium-Festuca complex and the use of SC to develop immortalized mapping populations for the dissection of a wide range of agronomically important traits. The germplasm available is a valuable practical resource and will aid understanding the basis of inbreeding depression and hybrid vigour in key temperate forage grass species.

CONCLUSIONS

A better understanding of the genetic control of additional SC loci offers new insight into SI systems, their evolutionary origins and their reproductive significance. Heterozygous outcrossing grass species that can be readily selfed facilitate studies of heterosis. Moreover, SC introduction into a range of grass species will enable heterosis to be exploited in innovative ways in genetic improvement programmes.

Fine mapping a self-fertility locus in perennial ryegrass

A self-fertility locus was fine mapped to a 1.6 cM region on linkage group 5 in a perennial ryegrass population. This locus was the main determinant of pollen self-compatibility. In grasses, self-incompatibility (SI) is characterized by a two-loci gametophytic (S and Z) mechanism acting together in the recognition and inhibition of self-pollen. Mutations affecting the expression of SI have been reported in a few grass species. In perennial ryegrass (Lolium perenne L.), a mutation independent from S and Z, and mapping on linkage group 5 (LG 5), was previously reported to produce self-fertile plants. Here, we describe fine mapping of the self-fertility (SF) gene in a perennial ryegrass population and determine whether there is any effect of other genomic regions on the pollen compatibility. The phenotypic segregation of SF showed a bimodal distribution with one mean at 49% pollen compatibility and the other at 91%. Marker-trait association analysis showed that only markers on LG 5 were significantly associated with the trait. A single gene model explained 82% of the observed variability and no effects of the other regions were detected. Using segregation and linkage analysis, the SF locus was located to a 1.6 cM region on LG 5. The flanking marker sequences were aligned to rice and Brachypodium distachyon reference genomes to estimate the physical distance. We provide markers tightly linked to SF that can be used for introgression of this trait into advanced breeding germplasm. Moreover, our results represent a further step towards the identification of the SF gene in LG 5.

A High-Density, Sequence-Enriched Genetic Map of Hordeum bulbosum and Its Collinearity to H. vulgare

L., a wild grass and close relative of cultivated barley ( L.), gained importance in plant breeding as inducer of haploid plants in crosses with barley and also as a genetic resource for introgression of disease resistance/tolerance genes into cultivated barley. Genetic mapping of genes introgressed from is a prerequisite for their efficient utilization in barley breeding, but often hindered due to repressed recombination. The mechanism underlying the reduced frequency or lack of meiotic recombination between . and . chromatin in introgressed segments is not understood. It may be explained by lack of genome collinearity or other structural differences between both genomes. In the present study, two F mapping populations of were analyzed by genotyping-by-sequencing (GBS) and four dense genetic maps containing 1449, 996, 720, and 943 SNP markers, respectively, revealed overall a high degree of collinearity for all seven homeologous linkage groups of and . The patterns of distribution of recombination along chromosomes differed between barley and , indicating organizational differences between both genomes.

A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population

Self-incompatibility (SI) is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3). These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with marker sequences on Lolium LGs 3 and 6 were also identified. We therefore demonstrate the power of a novel association genetics approach to identify the genes controlling multi-locus gametophytic SI systems and to identify novel loci potentially involved in already established SI systems.

Overcoming self-incompatibility in grasses: a pathway to hybrid breeding

Allogamous grasses exhibit an effective two-locus gametophytic self-incompatibility (SI) system, limiting the range of breeding techniques applicable for cultivar development. Current breeding methods based on populations are characterized by comparably low genetic gains for important traits such as biomass yield. To implement more efficient breeding schemes, the overall understanding of the SI system is crucial as are the mechanisms involved in the breakdown of SI. Self-fertile variants in outcrossing grasses have been studied, and the current level of knowledge includes approximate gene locations, linked molecular markers and first hypotheses on their mode of action. Environmental conditions increasing seed set upon self-pollination have also been described. Even though some strategies were proposed to take advantage of self-fertility, there have, so far, not been changes in the methods applied in cultivar development for allogamous grasses. In this review, we describe the current knowledge about self-fertility in allogamous grasses and outline strategies to incorporate this trait for implementation in synthetic and hybrid breeding schemes.

Assessing the allozyme variation in cultivars and Swedish landraces of rye (Secale cereale L.)

Genetic interpretation and diversity of 9 isozyme loci have been estimated in 7 improved varieties and 19 landraces from Sweden by means of starch gel electrophoresis. The isozyme systems were ACO, DIA, GPI, MDH, PGD and PGM. For the statistic analysis we used the following measures: average number of alleles per locus, percentage of polymorphic loci, average heterozygosity direct count and average heterozygosity Hardy-Weinberg expected unbiased estimate. The measures were made on species and population levels. The distribution of the total genetic diversity among populations was also calculated. To illustrate the genetic relationships among populations, genetic distances were measured and principal component analysis performed. As expected in a cross-pollinated crop we found high genetic diversity and a larger variation within than among the populations. Somewhat unexpectedly, however, we found that the currently used varieties have the same high level of heterozygosity as the landraces but in the dendrogram the two groups are separated. The dendrogram showed three main clusters. The large cluster included 21 populations and the two small clusters were clearly distinguishable from the rest. The landrace spring-type could not be separated from the landraces winter-type, but we did detect a difference between different spring types. A few populations had unique alleles for certain loci.

Genetic studies of self-fertility in rye (Secale cereale L.). 2. The search for isozyme marker genes linked to self-incompatibility loci

The segregation of several isozyme marker genes has been studied in F2 inbred families from hybrids between self-sterile and five self-fertile inbred lines (nos. 2, 3, 4, 5, and 8) as well as from interline hybrids. Self-pollination of F1 hybrids between self-sterile forms and lines 5 and 8 gave an F2 segregation ratio of 1 heterozygote:1 homozygote for the gene Prx7 (chromosome 1R) against the allele from the line. This is interpreted as a result of tight linkage of the Prx7 gene with the S1 gene in chromosome 1R (recombination at a level of 0-1%). The self-pollination of such hybrids with lines 2,3 and 4 gave normal segregation for the Prx7 gene (1:2:1). This means that these lines carry a self-fertility allele which is not on chromosome 1R. Interline hybrids 5×2, 5×3 and 5×4 had self-fertility alleles for the two S genes and in inbred F2 progenies gave the expected deviating segregation for the Prx7 gene in a ratio of 2:3:1. The segregation of interline hybrid 5×8 was normal, 1:2:1, as expected. Highly-deviating segregation in an inbred F2 family of a hybrid with line 5 has also been obtained for another gene from chromosome 1R - Pgi2 (recombination with the S1 locus of 16.7%). By using the same method it has been estimated that line 4 has a self-fertility allele of the S2 locus from chromosome 2R and that the genes β-Glu and Est4/11 are linked with it (recombination 16.7% and 17.5-20% respectively). Lines 2 and 3 have a self-fertility allele of the S5 locus from chromosome 5R which is linked with the Est5-7 gene complex (recombination at a level of 28.8-36.0%).

Genetic studies of self-fertility in rye (Secale cereale L.). 1. The identification of genotypes of self-fertile lines for the Sf alleles of self-incompatibility genes

Segregation for self-fertility has been studied in progenies from the crosses of self-sterile (SS) plants with interline hybrids obtained by a diallel scheme of pollinations between seven self-fertile (SF) lines (nos. 2-8) and with F1 (SS plant x SF line) hybrids. All the offspring families from the SS plant x F1 (SS plant x SF line) crosses demonstrated a 1SF∶1SS segregation. The crosses of SS plants with some interline hybrids gave only self-fertile plants, whereas the crosses with other interline hybrids gave a segregation of 3SF:1SS expected in the case of digenic segregation. The data obtained permitted us to identify three different S loci (S1, S2, S5) and to estimate the genotypes of self-fertile lines for their Sf alleles: lines 5, 6, 7 and 8 are S1f/S1f S2n/S2n S5m/S5m, line 4 is S1n/S1n S2f/S2f S5m/S5m, and lines 2 and 3 are S1n/S1n S2m/S2m S5f/S5f(Sn, Sm designate active alleles of the incompatibility genes). The identification of the particular S gene which is presented by the Sf allele in each line has been made on the basis of our data concerning the linkage of the Sf mutation with isozyme markers of particular rye chromosomes, which is reported in an accompanying paper.

Stability of self-incompatibility systems

Multi-locus self-incompatibility systems offer few obvious adaptive advantages to the species possessing them. However, the gametophytic system's independent gene action allows the separate genes in a two gene system to behave as if they were individually not involved in a systematic disruption of panmixia. Under such circumstances, fixation of one of the two genes is readily obtained if an allele possesses a selective advantage. The resulting single gene system (the classic Nicotiana system) is then resistant to disruption, except by genes which allow selfing, which rapidly reach fixation.

Absence of qualitative genes controlling interspecific pairing in rye B chromosomes

The meiotic behaviour of hybrids between Secale cereale carrying B chromosomes and S. vavilovii has been studied in order to estimate the effects of B chromosomes on hybrid meiotic pairing. The possible effect of Bs on the meiotic pairing of the offspring from backcrosses with S. vavilovii has been studied also. The results obtained clearly indicate that no detectable differences existed in chromosome pairing of hybrids with or without B chromosomes. The hypothetical existence of epistatic genes on cereale genome masking the effect of Bs has been rejected after the results obtained in backcrosses. Therefore, lack of qualitative genes controlling interspecific pairing on rye B chromosomes has been concluded. A quantitative effect of B chromosomes was detected only when they were in alien cytoplasm.

The transmission of rye B chromosomes in natural pollination

This paper examines the transmission of B chromosomes in natural (but controlled) pollination, in order to obtain results which can be applied to natural populations of rye. The frequencies of the female gametes in both 2n= 14+1 and 2n=14+2 rye plants have been estimated with reference to their chromatid constitution. From the results obtained on the offspring, it seems that preferential distribution takes place during female meiosis of 2n= 14+2 plants. It has been demonstrated that pollen carrying B chromosomes formed in plants of 2n=14+2 was more competitive than normal pollen. On the contrary, when it was formed from plants 2n=14+1, B chromosome elimination by pollen was total. This process may be considered as sporophytic determination. The genetic significance of the presence of B chromosomes in natural populations is discussed. It is proposed that B chromosomes may be the cytological expression of a complex evolutionary system which results in conservation of population genetic variability.

Heritability of some characters of rye under open pollination

Present investigations cover the correlation between four characters of maternal plants of rye and the corresponding characters in their offspring. Tabulated results pertain to four two-year periods for the Exp. Sta. Choryń and two such periods for the Exp. Sta. Laski, involving several plant material groups derived from various crosses with Dańkowskie Selekcyjne rye.The effects of average grain weight per ear of the maternal plant on the corresponding yields in the offspring have proved rather small, but sporadically approaching or attaining the limits of significance. The influence of resistance to lodging of the maternal plant on that same character in the offspring has proved no greater, but, in spite of the considerable multidirectional differentiation of the coefficients of correlation and regression, in 4 groups out of a total of 27 they surpassed the limits of significance, sometimes attaining high values.In contrast to these two characters, but in agreement with expectations, there was a fairly pronounced effect of 1000 grain weight and of the maternal plant height on the same characters in the offspring. Significant coefficients of regression for the former characters ranged from 0.11 to 0.22 g, and for the latter from 0.03 to 0.37 cm.The present paper also includes less numerous results of analogous investigations on the relation of characters determined in the microtrials with those examined in the next generation. These results indicate good transmission of earliness, measured by the date of earing, and of the weight of 1000 grains, but a much weaker transmission of resistance to lodging and of grain yields.The conclusions drawn on breeding strategy suggest opportunities for efficient selection under the method of recombination towards short straw and a high 1000 grain weight within maternal plants, and also the advisability of shifting the main impact of selection for yield and resistance to lodging onto the following generations.