Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Population structure and genetic diversity of a germplasm for hybrid breeding in rye (Secale cereale L.) using high-density DArTseq-based silicoDArT and SNP markers

Investigating genetic structure and diversity is crucial for the rye hybrid breeding strategy, leading to improved plant productivity and adaptation. The present study elucidated the population structure and genetic diversity of 188 rye accessions, comprising 94 pollen fertility restoration lines (RF) and 94 cytoplasmic male-sterile (CMS) lines with Pampa sterilizing cytoplasm using SNP and silicoDArT markers from the diversity array technology (DArT)-based sequencing platform (DArTseq). Expected heterozygosity (H_e) and Shanon's diversity (I) indexes varied slightly between marker systems and groups of germplasms (H_e = 0.34, I = 0.51 for RF and CMS lines genotyped using SNPs; H_e = 0.31, I = 0.48, and H_e = 0.35, I = 0.53 for RF and CMS using silicoDArTs, respectively). ANOVA indicated moderate variation (7%) between RF and CMS breeding materials. The same parameter varied when chromosome-assigned markers were used and ranged from 5.8% for 5R to 7.4% for 4R. However, when silicoDArT markers were applied, the respective values varied from 6.4% (1R) to 8.2% (3R and 4R). The model-based (Bayesian) population structure analysis based on the total marker pool identified two major subpopulations for the studied rye germplasm. The first one (P1) encompasses 93 RF accessions, and the second one (P2) encompasses 94 CMS and one RF accession. However, a similar analysis related to markers assigned to selected chromosomes failed to put plant materials into any of the populations in the same way as the total marker pool. Furthermore, the differences in grouping depended on marker types used for analysis.

Genomic Scan of Male Fertility Restoration Genes in a 'Gülzow' Type Hybrid Breeding System of Rye (Secale cereale L.)

Efficient and stable restoration of male fertility (Rf) is a prerequisite for large-scale hybrid seed production but remains an inherent issue in the predominant fertility control system of rye (Secale cereale L.). The ‘Gülzow’ (G)-type cytoplasmic male sterility (CMS) system in hybrid rye breeding exhibits a superior Rf. While having received little scientific attention, one major G-type Rf gene has been identified on 4RL (Rfg1) and two minor genes on 3R (Rfg2) and 6R (Rfg3) chromosomes. Here, we report a comprehensive investigation of the genetics underlying restoration of male fertility in a large G-type CMS breeding system using recent advents in rye genomic resources. This includes: (I) genome-wide association studies (GWAS) on G-type germplasm; (II) GWAS on a biparental mapping population; and (III) an RNA sequence study to investigate the expression of genes residing in Rf-associated regions in G-type rye hybrids. Our findings provide compelling evidence of a novel major G-type non-PPR Rf gene on the 3RL chromosome belonging to the mitochondrial transcription termination factor gene family. We provisionally denote the identified novel Rf gene on 3RL RfNOS1. The discovery made in this study is distinct from known P- and C-type systems in rye as well as recognized CMS systems in barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We believe this study constitutes a stepping stone towards understanding the restoration of male fertility in the G-type CMS system and potential resources for addressing the inherent issues of the P-type system.

New PCR-specific markers for pollen fertility restoration QRfp-4R in rye (Secale cereale L.) with Pampa sterilizing cytoplasm

Pampa cytoplasmic male sterility phenomenon is used extensively in the rye hybrid breeding programs. It relies on sterilizing action of the cytoplasm resulting in non-viable pollen of female lines. The sterilizing effect is problematic for reversion, and efficient restores are needed. The most promising QTL is located on chromosome 4R, but other chromosomes may also code the trait. Advanced recombinant inbred lines formed bi-parental mapping population genotyped with DArTseq markers. Genetic mapping allowed the seven linkage groups to construct with numerous markers and represent all rye chromosomes. Single marker analysis and composite interval mapping were conducted to identify markers linked to the pollen fertility. Association mapping was used to detect additional markers associated with the trait. A highly significant QTL (QRfp-4R) that explained 42.3% of the phenotypic variation was mapped to the distal part of the long arm of the 4R chromosome. The markers localized in the QRfp-4R region achieve R² association values up to 0.59. The homology of the 43 marker sequences to the loci responsible for fertility restoration in other species and transcription termination factor (mTERF) linked to Rf genes was established. Ten markers were successfully converted into PCR-specific conditions, and their segregation pattern was identical to that of unconverted DArTs.