A comprehensive understanding of CMS/Rf system enabled by modern omics tools and technologies considerably improves our ability to harness hybrid technology for enhancing the productivity of field crops.
 Harnessing hybrid vigor or heterosis is a promising approach to tackle the current challenge of sustaining enhanced yield gains of field crops. In the context, cytoplasmic male sterility (CMS) owing to its heritable nature to manifest non-functional male gametophyte remains a cost-effective system to promote efficient hybrid seed production. The phenomenon of CMS stems from a complex interplay between maternally-inherited (mitochondrion) and bi-parental (nucleus) genomic elements. In recent years, attempts aimed to comprehend the sterility-inducing factors (orfs) and corresponding fertility determinants (Rf) in plants have greatly increased our access to candidate genomic segments and the cloned genes. To this end, novel insights obtained by applying state-of-the-art omics platforms have substantially enriched our understanding of cytoplasmic-nuclear communication. Concomitantly, molecular tools including DNA markers have been implicated in crop hybrid breeding in order to greatly expedite the progress. Here, we review the status of diverse sterility-inducing cytoplasms and associated Rf factors reported across different field crops along with exploring opportunities for integrating modern omics tools with CMS-based hybrid breeding.

Cytoplasmic male sterility (CMS) in hybrid breeding in field crops

Development of core collections is an effective tool to extensively characterize large germplasm collections, and the use of a mini-core subsampling strategy further increases the effectiveness of genetic diversity analysis at detailed phenotype and molecular levels. We report the formation of a mini-core subset containing 217 entries derived from 1794 core entries representing the genetic diversity found in more than 18,000 accessions of the USDA-ARS rice (Oryza sativa L.) germplasm collection. The mini-core was developed with PowerCore software on the basis of 26 phenotypic traits and 70 molecular markers. The 217 entries in the mini-core had a similar distribution over 15 geographical regions, with 1794 entries in the original core collection. The resultant mini-core had 6.3% of mean difference (MD%), 16.5% of variance difference (VD%), 102.7% of variable rate (VR%), and 97.5% of coincidence rate (CR%) with the core collection, which brought about full coverage of 26 traits. All 962 alleles identifi ed by the 70 markers in the core collection were captured in the mini-core, which maximized allelic richness up to 100% and resulted in an average genetic diversity (Nei index) of 0.76, ranging from 0.37 to 0.97 among the markers. In conclusion, the mini-core presented in this study is a highly suitable and representative subset of the USDA rice core collection as well as the entire USDA-ARS rice germplasm holdings. Univ. of Arkansas, Rice Research and Extension Center, 2900 Highway 130E, Stuttgart, AR 72160. Received 22 Sept. 2008. *Corresponding author (hagrama@uark.edu). Abbreviations: ASV, alkali spreading value; CR%, coincidence rate; MD%, mean diff erence; PCR, polymerase chain reaction; QTL, quantitative trait loci; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; VD%, variance diff erence; VR%, variable rate.

https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2135/cropsci2008.06.0551er

Genetic Assessment of a Mini-Core Subset Developed from the USDA Rice Genebank

The review outlines past failures, present status and future prospects of hybrid wheat, and includes information on CMS/CHA/transgenic approaches for male sterility, heterotic groups and cost-effective hybrid seed production. Hybrid varieties give increased yield and improved grain quality in both cross- and self-pollinated crops. However, hybrid varieties in self-pollinated crops (particularly cereals) have not been very successful, except for hybrid rice in China. In case of hybrid wheat, despite the earlier failures, renewed efforts in recent years have been made and hybrid varieties with desirable attributes have been produced and marketed in some European countries. This review builds upon previous reviews, with a new outlook and improved knowledge base, not covered in earlier reviews. New technologies have been described, which include the Hordeum chilense-based CMS–fertility restorer system, chromosomal XYZ-4E-ms system and the following transgenic technologies: (1) conditional male sterility involving use of tapetum-specific expression of a gene that converts a pro-toxin into a phytotoxin causing male sterility; (2) barnase-barstar SeedLink system of Bayer CropScience; (3) split-barnase system that obviates the need of a barstar-based male restorer line; and (4) seed production technology of DuPont-Pioneer that makes use of transgenes in production of male-sterile lines, but gives hybrid seed with no transgenes. This review also includes a brief account of studies for discovery of heterotic QTL, genomic prediction of hybrid vigour and the development of heterotic groups/patterns and their importance in hybrid wheat production. The problem of high cost of hybrid seed due to required high seed rate in wheat relative to hybrid rice has also been addressed. The review concludes with a brief account of the current efforts and future possibilities in making hybrid wheat a commercial success.

Hybrid wheat: past, present and future.

With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC–MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa.

/pdf/the-patterns-of-population-differentiation-in-a-brassica-2xfgg2nfbq.pdf

The patterns of population differentiation in a Brassica rapa core collection

Genetic diversity of a set of 71 wheat accessions, including 53 biotype 2 Russian wheat aphid (RWA2)-resistant landraces and 18 RWA2 susceptible accessions, was assessed by examining molecular variation at multiple microsatellite (SSR) loci. Fifty-one wheat SSR primer pairs were used, 81 SSR loci were determined, and 545 SSR alleles were detected. These SSR loci covered all the three genomes, 21 chromosomes, and at least 41 of the 42 chromosome arms. Diversity values averaged over SSR loci were high with mean number of SSR alleles/locus = 6.7, mean Shannon’s index (H) = 1.291, and mean Nei’s gene diversity (He) = 0.609. The three wheat genomes ranked as A > D > B and the homoeologous groups ranked as 7 > 3 > 1 > 2 > 6 > 5 > 4 based on the number of alleles per locus. Xgwm136 on chromosome arm 1AS is the most polymorphic SSR locus with the largest number of observed and effective alleles and the highest H and He. Among all 2485 pairs of wheat accessions, genetic distance (GD) ranged from 0.054 to 1.933 and averaged 0.9832. A dendrogram based on GD matrix showed that all the wheat accessions could be grouped into distinct clusters. Most of the susceptible cultivars (13/18) were clustered into groups that contains all or mostly susceptible accessions. Most of the U.S. cultivars belong to a group that is distinguishable from all the different RWA2 resistant groups. Diversity analysis was also conducted separately for subgroups containing 53 RWA2-resistant accessions and 18 RWA2-susceptible accessions. Association mapping revealed 28 SSR loci significantly associated with leaf chlorosis, and 8 with leaf rolling. New chromosome regions associated with RWA2 resistance were detected, and indicated existence of new RWA resistance genes located on chromosomes of all other homoeologous groups in addition to the groups 1 and 7 in bread wheat. This information is helpful for development of mapping populations for RWA2 resistance genes from different phylogenetic groups, and for wise utilization of the RWA-resistant germplasm in wheat breeding programs.

/pdf/microsatellite-based-molecular-diversity-of-bread-wheat-2lvxwr143r.pdf

Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid.

An agronomic gene pool of wheat (Triticum aestivum L.) was constructed through recurrent selection. In present research, 24 wheat SSR markers determining 25 loci on 14 different chromosomes were used to evaluate the gene pool. Thirty parents used as original materials in recurrent selection were also assessed. In total, 115 alleles were detected in gene pool with an average of 4.6, ranging from 2 to 9 alleles per locus. Statistical test showed that genetic diversities had no significant difference between the gene pool and the 30 parents. Principle coordinates analysis revealed that the individuals of the gene pool were mainly divided into three groups, which was consistent with the result of cluster analysis based on genetic distance matrix of the gene pool. Cluster analysis was carried out based on Euclidian distance calculated upon five morphological trait values and the results showed that most individuals were in a group while the others scattered. Correlation analysis of genetic distance matrix and Euclidian distance matrix showed no significant correlation between two matrices. The results suggest that the gene pool is improved after several cycles of selection, while genetic variation is still maintained. Therefore, the gene pool is suitable for further breeding program.

Genetic diversity of wheat gene pool of recurrent selection assessed by microsatellite markers and morphological traits

A new cytoplasmic male-sterile (CMS) system for hybrid wheat breeding, YA-type CMS line with the cytoplasmic mutant from the common wheat variety 'CA8057', was developed by the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. The pollen sterility of YA-type CMS line was easily maintained but difficult to restore. Some sterile lines with desirable agronomic performance, such as msYA-'CA8057' (BC 17 ), msYA-'Yuandong 6' (BC 9 ), msYA-'Jin 411'(BC 9 ), msYA-'WLI' (BC 10 ), msYA-'Yanshi 9' (BC 10 ), msYA-'BPml6' (BC 9 ), msYA-'Jindong 8' (BC 9 ) and msYA-'Jinmai 33' (BC 9 ), were bred and a restorer line GR1 was screened with 26 new restorer lines being developed by transferring restorer genes from GR1. It was found that abnormal phenomena occurred at the uninucleate-pollen stage and the abortive pollen was poor in starch content and other components. The variance analysis of agronomic traits in eight sterile lines indicated that there was no general negative effect of cytoplasm. The genetic analysis for fertility restoration showed that two pairs of independent major genes (designated YARf 1 YARf 1 YArf 2 YArf 2 ) and some minor genes could be involved in the fertility restoration in restorer line GR1, and YARf 1 was epistatic over YARf 2 for the genetic effect of fertility restoration. As a new CMS system, the YA-type CMS line was of potential value for hybrid wheat breeding and should be further studied.

A YA-type cytoplasmic male-sterile source in common wheat

'Yi 4060' is an elite restorer line of a non-photoperiod-sensitive D 2 -type cytoplasmic male-sterile (CMS) line of wheat. Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were employed to map one major fertility-restoring gene (D 2 Rf 1 ) in 'Yi 4060'. The sterile and fertile DNA pools were established from individuals in BC 6 , based on bulked segregant analysis. One RAPD marker E09, linked to D 2 Rf 1 , was converted to a SCAR marker and designated as E09-SCAR 865 . The genetic distance between E09-SCAR 865 and D 2 Rf 1 is 9.5 cM. Two SSR markers, Xgwm11 and Xgwm18, were also linked to a D 2 Rf 1 and co-segregated with E09-SCAR 865 . The three molecular markers are useful in marker-assisted breeding of the elite restorer lines for D 2 -type CMS lines in wheat.

SSR and SCAR markers linked to the fertility-restoring gene for a D2-type cytoplasmic male-sterile line in wheat

The invention discloses a method of male sterility in plant by artificial hybridization, which is characterized in that: the method is a method which inhibits the expression of an endogenous HSP70 gene of plant anther through the antisense RNA technology, and interferes the normal growth of the transgenic plant anther so as to acquire a male sterility transgenic plant. In particular, the method isa method which transforms an antisense RNA expression vector of the HSP70 gene driven by an Osg6B promoter expressed by anther specificity into a graminaceous plant, inhibits the expression of the endogenous HSP70 gene of the anther, and interferes the normal growth of the transgenic plant anther so as to acquire the male sterility transgenic plant. The transgenic plant acquired by the method canimplement male complete sterility.

Method for artificially creating plants male sterility

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Genetic diversity of wheat gene pool of recurrent selection assessed by microsatellite markers and morphological traits

A YA-type cytoplasmic male-sterile source in common wheat

SSR and SCAR markers linked to the fertility-restoring gene for a D2-type cytoplasmic male-sterile line in wheat

Method for artificially creating plants male sterility