Anonymous and gene-linked microsatellite markers reveal no correlation between heterozygosity and song complexity in a wild population of song sparrows

ABSTRACT Correlations between heterozygosity and fitness are commonly reported in the literature, but there is disagreement about the frequency of such correlations and the mechanisms which underlie them. Using a multi-year data set acquired from a wild population of song sparrows I investigated the relationship between heterozygosity and song complexity, an important sexually selected trait thought to be an indicator of genetic quality. Heterozygosity was determined at 17 putatively neutral microsatellites and 5 microsatellites derived from the expressed sequence tag of zebra finch brain proteins. Song and syllable repertoire size were taken as measures of song complexity. Neither genetic marker type was predictive of song complexity. A further test failed to support the hypothesis that heterozygosity-fitness correlations at marker loci are due to closely linked coding genes. These results indicate that heterozygosity is unlikely to play a major role in individual song complexity in this outbred population of song sparrows

Plant Genetics and Biotechnology in Biodiversity

Plant genetic resources for food and agriculture (PGRFA) have been collected and exchanged for centuries. The rapid development of novel tools for genetic and phenotypic analysis is changing the way we can uncover diversity and exploit its value in modern agriculture. The integration of novel analytical tools is crucial for translating research into much-needed, more efficient management and use of PGRFA. This Special Issue provides an overview of recent topics on plant genetics and biotechnology in biodiversity. The proposed reviews and research papers present current trends and examples of genetic resources’ description, conservation, management, and exploitation, highlighting that new approaches and methodogies can increase our understanding and efficient use of PGRFA to address the agricultural challenges that lie ahead

Toadal Isolation: Genetic Connectivity of the Western Toad (Anaxyrus boreas) along I-90 in the Snoqualmie Pass Area of Washington State

Single-nucleotide polymorphisms (SNPs) were used to assess the genetic connectivity of western toad (Anaxyrus boreas) breeding populations along Interstate-90 near Snoqualmie Pass, WA. Sites north and south of the freeway were sampled during the breeding season of 2019. SNP loci were subsequently generated using the proprietary DArTseqTM (Canberra, ACT, Australia) method. A total of 15,468 SNPs were used to calculate pairwise FST values and three distinct breeding populations were identified, two north and one south of I-90. All pairwise FST values between these sites were low (0.02) but significantly different from 0. The lowest pairwise FST was between the two sites that were furthest apart (11.6 km), indicating higher levels of connectivity along than across the freeway. A de novo discriminant analysis of principal components (DAPC) confirmed this division between sites on either side of I-90. Although I-90 is the most prominent potential barrier on the landscape, the Yakima River may also be contributing to this division. An a priori DAPC was able to distinguish between all populations with enough confidence to assign toads that were randomly encountered in the summer of 2019 to their most likely population of origin and will be a useful tool in future studies

Genetic improvement of grain yield and quality in rice (Oryza sativa L.) in South Sudan.

Doctor of Philosophy in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg, 2017.Abstract available in PDF file

Biosystematics and phenology of Alnus maritima (Betulaceae)

Alnus maritima (Marsh.) Muhl. ex Nutt. (seaside alder) is a rare woody plant species found naturally in only three small disjunct populations in the United States. Concern for the conservation of A. maritima and questions regarding the proper classification of its disjunct populations have generated a need for information concerning its ecology and biosystematics, while growing interest in the use of A. maritima in managed landscapes has demonstrated the need for information concerning its ecophysiology and landscape fitness. My first objective was to recount the taxonomic and horticultural history of A. maritima and to report on its current landscape usage and cultivation. Although it has received little attention from horticulturists since its introduction into cultivation over 100 years ago, A. maritima is now being recognized as a stress-resistant large shrub or small tree. My second objective was to derive the infraspecific systematics of A. maritima by morphometric analysis and to classify the three disjunct populations properly. Taxonomic distances were compatible with the modern definition of subspecies, and the subspecific epithets oklahomensis, georgiensis, and maritima were given the three taxa. My third objective was to characterize the molecular systematics of A. maritima according to ISSR polymorphisms. The molecular phylogeny of eight species of Alnus confirmed that A. maritima is most closely related to the other members of subg. Clethropsis and was the first member of its subgenus to diverge. At the infraspecific level, molecular and morphometric phylogenies agreed and showed that subsp. oklahomensis was the first to diverge. My fourth objective was to characterize the cold hardiness of A. maritima in native habitats and in colder climates. Analyses showed that the subspecies are similar in cold hardiness, that plants from all three subspecies can survive mid-winter extremes as low as -80°C, and that cold acclimation differs between plants grown in colder climates and those in native habitats. Results from these studies support the theory that A. maritima originated in Asia, migrated into North America across the Bering land bridge, and was established over a large range before being forced into its present meager distribution

Genetic diversity and relationship of mango and its wild relatives (Mangifera spp.) based on morphological and molecular markers

Mango andits wild relatives (Mangifera spp.) are essential for future mango breeding, including preservation programs, because they provide many beneficial genes (agronomic traits), particularly those related to resistance to biotic and abiotic stressors. However, there is a limited understanding of the genetic diversity and relationships of this germplasm. This study aimed to determine the diversity and relationship between endemic mango and its wild relatives (Mangifera spp.) from Borneo Island, Indonesia, using leaf morphology and the internal transcribed spacer (ITS) region. Fifteen samples of Mangifera, covering 12 species, were used. Morphologically, the endemic Mangifera had a low diversity of only 0.22. Based on the ITS sequence, Mangifera endemic to Borneo had a high level of genetic diversity (0.069). In addition, this sequence had a total variable number of 215 bp, of which 110 bp were singleton sites, 89 informative parsimony and 41 indels. Phylogenetic analysis showed that Mangifera was grouped into three clusters for leaf morphological traits and four clades for the ITS region. In this case, the furthest relationship was pointed out by ‘Hampalam’ (M. laurina) and ‘Tambusui’ (M. macrocarpa), as well as by ‘Rawa-Rawa’ (M. similis) and ‘Samputar’ (M. torquenda). In contrast, the closest relationship was shown by ‘Hambawang Damar’ (M. foetida) and ‘Hambawang Puntara’ (M. foetida), including ‘Samputar’ (M. torquenda) and ‘Pauh’ (M. quadrifida). In particular, the common mango (M. indica) was closely related to ‘Asam Buluh’ and ‘Hampalam’ (M. laurina) and distantly related to ‘Pauh’ (M. quadrifida)and ‘Rawa-Rawa’ (M. similis

Breeding dual-purpose Sweetpotato [Ipomoea batatas (L.) Lam.] varieties in Rwanda.

Doctor of Philosophy in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg 2017.Sweetpotato [Ipomoea batatas (L.) Lam] is a multi-purpose crop where the fresh roots are used for human food and aboveground biomass for animal feed. In Rwanda, sweetpotato plays a key role in the mixed crop-livestock farming systems providing economic opportunities from livestock and crop production enterprises. However, dual-purpose sweetpotato varieties (DPSVs) with farmer-preferred traits and enhanced yields are yet to be developed and deployed in sub-Saharan Africa including in Rwanda. Therefore, the objectives of this study were: (i) to assess the role of sweetpotato in the crop-livestock farming system practised in Rwanda, to identify farmer-preferred traits and to establish farmer-led priorities in breeding dual-purpose sweetpotato varieties, (ii) to assess the level of phenotypic diversity present among sweetpotato varieties grown in Rwanda, and to select suitable parents for breeding DPSVs, (iii) to characterize diverse sweetpotato germplasm using simple sequence (SSR) markers to identify potential parents for breeding DPSVs, and (iv) to determine gene action and heritability of storage root and aboveground biomass yields, and yield components, in sweetpotato varieties, and to undertake early clonal selections for future release of DPSVs. In the first study, a participatory rural appraisal (PRA) was undertaken in the following three selected districts of Rwanda: Bugesera, Huye and Nyagatare. Data were collected through semi-structured interviews, focus group discussions and a transect walk. All respondents wanted to grow new sweetpotato varieties with improved storage root production combined with high aboveground biomass. About 87.7, 66.6 and 51.1% of the respondents indicated that root-related traits of the crop such as high dry matter content, red skin colour and yellow flesh colour were additional preferred traits, respectively. Secondly, fifty one diverse sweetpotato genotypes were evaluated in field trials conducted at the Rubona and Karama experimental stations of the Rwanda Agriculture Board (RAB) using a 6 x 9 unbalanced alpha lattice design with three replications. The top two genotypes selected for their high yields of storage roots were RW11-4923 and RW11-2419, with yields of 20.91 t.ha-1 and 20.18 t.ha-1, respectively. The genotypes RW11-4923 and Wagambolige were the best performers for aboveground yields, producing 23.67 t.ha-1 and 23.45 t.ha-1 of vines, respectively. The genotype Ukerewe performed well for its dry root yield (7.09 t.ha-1), while RW11-4923 had the highest mean dry vine yield (5.17 t.ha-1). The genotypes RW11-2910 and 8-1038 had root-to-vine ratios of 2.0 and 1.5, respectively. Two main phenotypic groups with 10 sub-groups were detected through cluster analysis and 24 sweetpotato clones were selected for their combination of high storage root yields, heavy vine production and prolific flowering ability. Thirdly, the above 24 selected sweetpotato genotypes were genotyped with nine highly polymorphic SSRs. Cluster analysis allocated the test genotypes into three distinct genetic groups: I, II and III, with 6, 5 and 13 genotypes, respectively. Eight genetically diverse clones were selected, namely SPK004 and K5132/61 (from Group I), 4-160, Ukerewe, RW11-2910 (Group II), RW11-1860, Wagabolige, 2005-179 (Group III), with key agronomic traits for breeding DPSVs. Finally, a half-diallel mating design was used and crosses were performed involving eight parents selected for their complementary traits including storage root and aboveground biomass production, dry matter content and farmer-preferred traits. A total of 28 families and 8 parents were field evaluated at Rubona, Karama and Ngoma research stations of RAB. Families had highly significant (P < 0.001) differences for fresh root yield (FRY), root dry matter content (RDMC), dry root yield (DRY), fresh vine yield (FVY), vine dry matter content (VDMC), dry vine yield (DVY), total biomass on dry weight basis (TBDW), root-to-vine ratio (R:V) and harvest index (HI). The general combining ability (GCA) and specific combining ability (SCA) effects were significant for FRY, RDMC, DRY, R:V, HI and VDMC. The GCA/SCA ratios were 0.75, 0.81 and 0.88 for DRY, RDMC and FRY, respectively, suggesting that additive gene action was more important than non-additive gene action in the expression of these parameters. Conversely, the GCA/SCA ratio was relatively lower, ranging between 0.09 and 0.28 for vine and root-vine combined parameters, suggesting that the non-additive component of the genetic variance, either dominance or epistasis, was more influential in controlling the traits. This implies that parental performance cannot necessarily be the basis of progeny performance prediction for these traits. The broad-sense heritability (H2) values were above 0.5 for all assessed traits, with FRY, HI and RDMC having higher estimates of 0.80, 0.81 and 0.92, in that order. RDMC had a high narrow-sense coefficient of genetic determination (NSCGD) of 0.80, while this parameter varied between 0.09 and 0.49 for the rest of the tested traits. The parent K5132/61 was the best combiner for FRY and HI, while the parents RW11-1860, RW11-2910, SPK004 and Ukerewe were best general combiners for RDMC. The parent Wagabolige was the best general combiner for FRY, DRY and R:V. Based on desirable SCA effects for FVY, DVY, TBDW, RDMC, R:V and FRY, the most promising families selected in this study were K5132/61 x Wagabolige, 4-160 x 2005-179, K5132/61 x RW11-1860 and RW11-2910 x 2005-179. Overall, the study developed promising families with high storage root and aboveground biomass yields. From these families, novel progenies were selected and are recommended for advanced clonal selection across multiple sites to release DPSVs in Rwanda or similar agro-ecologies in SSA