A multi-part strategy for introgression of exotic germplasm into elite plant breeding programs using genomic selection

Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.

Advances and outlook of horticultural bioengineering

A Branch of modern biotechnology for creating unique relevant genotypes is bioengineering that harnesses a spectrum of plant genome modification technologies. The study aimed to analyse the current state of the art in genome modification of fruit and berry crops for more significant (vs. premium pure breeding varieties) deviations of norm in the traits and properties of biotic and abiotic resistance, productivity, fruit quality, etc. First horticultural crop transformation studies aimed at developing protocols based on selectable enzyme marker genes of phosphorylationmediated aminoglycoside antibiotics detoxification. Neomycin phosphotransferase nptII constitutes the most common system of transgenic fruit and berry crop selection. In pome crops, the transgenic selection priorities were resistance to scab (Venturia inaequalis (Wint.) Cke), rust (Gymnosporangium juniper-virginianae Schwein.) and bacterial blight (Erwinia amylovora Burrill, Winslow et al.), higher fruit quality, including bright colouring, and reduced enzymatic browning. In stone crops, it was tolerance to plum pox (PPV), papaya ringspot (PRSV) and Prunus necrotic ringspot (PNRSV) viruses. In berry crops — resistance to Sphaerotheca humuli (DC.) Burrill fungus, grey mould (Botrytis cinerea Pers.), root rot (Phytophthora cactorum (Lebert & Cohn) J.Schrot.) and powdery mildew (Oidium tuckeri Berkeley), as well as higher fruit quality. In citruses — resistance to bacterial canker (Xanthomonas citri sub sp.), citrus ulcer (Xanthomonas axonopodis pv citri), greening disease (Huanglongbing (HLB)) and fungi (Trichoderma harzianum Rifai). In tropical crops — resistance to papaya ringspot (PRSV) and banana streak (eBSV) viruses. Unique FT-phenotype transgenic fruit lines are leveraged in the new FasTrack breeding strategy. Nine fruit and berry transgenic crop lines have now been registered worldwide. Transgenic Arctic apples (Golden, Granny, Fuji), plums (Honey Sweet) and papaya (Rainbow, SunUp, Laie Gold) are industry-approved in fresh and processed form. The transgenic list regulated in the Russian Federation does not include fruit or berry crops.

Designing the best breeding strategy for Coffea canephora: Genetic evaluation of pure and hybrid individuals aiming to select for productivity and disease resistance traits

Breeding programs of the species Coffea canephora rely heavily on the significant genetic variability between and within its two varietal groups (conilon and robusta). The use of hybrid families and individuals has been less common. The objectives of this study were to evaluate parents and families from the populations of conilon, robusta, and its hybrids and to define the best breeding and selection strategies for productivity and disease resistance traits. As such, 71 conilon clones, 56 robusta clones, and 20 hybrid families were evaluated over several years for the following traits: vegetative vigor, incidence of rust and cercosporiosis, fruit ripening time, fruit size, plant height, canopy diameter, and yield per plant. Components of variance and genetic parameters were estimated via residual maximum likelihood (REML) and genotypic values were predicted via best linear unbiased prediction (BLUP). Genetic variability among parents (clones) and hybrid families was detected for most of the evaluated traits. The Mulamba-Rank index suggests potential gains up to 17% for the genotypic aggregate of traits in the hybrid population. An intrapopulation recurrent selection within the hybrid population would be the best breeding strategy because the genetic variability, narrow and broad senses heritabilities and selective accuracies for important traits were maximized in the crossed population. Besides, such strategy is simple, low cost and quicker than the concurrent reciprocal recurrent selection in the two parental populations, and this maximizes the genetic gain for unit of time.

Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs

Background The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating—including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction—for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity. Results Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests’ moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community. Conclusions Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals.

Migration distance affects how closely Eurasian wigeons follow spring phenology during migration

Background The timing of migration for herbivorous migratory birds is thought to coincide with spring phenology as emerging vegetation supplies them with the resources to fuel migration, and, in species with a capital breeding strategy also provides individuals with energy for use on the breeding grounds. Individuals with very long migration distances might however have to trade off between utilising optimal conditions en route and reaching the breeding grounds early, potentially leading to them overtaking spring on the way. Here, we investigate whether migration distance affects how closely individually tracked Eurasian wigeons follow spring phenology during spring migration. Methods We captured wigeons in the Netherlands and Lithuania and tracked them throughout spring migration to identify staging sites and timing of arrival. Using temperature-derived indicators of spring phenology, we investigated how maximum longitude reached and migration distance affected how closely wigeons followed spring. We further estimated the impact of tagging on wigeon migration by comparing spring migratory timing between tracked individuals and ring recovery data sets. Results Wigeons migrated to locations between 300 and 4000 km from the capture site, and migrated up to 1000 km in a single day. We found that wigeons migrating to more north-easterly locations followed spring phenology more closely, and increasingly so the greater distance they had covered during migration. Yet we also found that despite tags equalling only around 2% of individual’s body mass, individuals were on average 11–12 days slower than ring-marked individuals from the same general population. Discussion Overall, our results suggest that migratory strategy can vary dependent on migration distance within species, and even within the same migratory corridor. Individual decisions thus depend not only on environmental cues, but potentially also trade-offs made during later life-history stages.

Abundance, Distribution, Morphometric, Feeding Evaluation and the Reproductive Strategies of Gymnarchus niloticus in the Lower River Niger at Agenebode, Edo State Nigeria

The study of the numerous areas of biology of fish produces ample and relevant information that aids scientist to explore, know and maintain the survival, growth, continuity and sustainability of life of various fish species. A total of 94 specimens of Gymnarchus niloticus were collected from River Niger at Agenebode during the sample period that ranged from 14 – 94 cm total length (54.88± 17.92); weighed 424 - 2281g (1569.61 ± 422.85). The length weight relationship (LWR) of G. niloticus in this study showed a negative (b<3) allometric growth pattern. Out of the 94 specimens analysed 54 males and 40 females were examined with a ratio of 1:1.4. Insects and decapods were the major food of the juveniles of Gymnarchus niloticus while the major food of preference of the sub adults and adults were Fish and insects with 27.12%, and 27.97% by FO. Gymnarchus niloticus possesses a single ovary in the female and single testis in the male which is often referred to as unpaired gonad. Fecundity ranged between 620 to 1378 eggs with a mean of 957.69 ± 112.31 eggs in females. The relationship between fecundity (F) and weight (W) and fecundity and standard length (SL) showed that fecundity is more related to weight than length of fish. Log F = 820.66 + 0.11 W and Log F = 151.23 + 5.31 SL. Fecundity had a positive significant correlation (P<0.05) with both somatic weight (r = 0.714) and standard length (r = 0.657) of fish. Ova diameter showed a ranged between 3.5 and 7.9 mm with a mean of 4.72 ± SD1.69 mm and it had significant relationship (P<0.05) with total weight, gonad weight and maturity stage. Gymnarchus niloticus in the Lower River Niger at Agenebode showed that G. niloticus has an unpaired gonad in both sexes, a gonochoristic reproductive pattern. Fecundity is low and the ova are large. They are small brood spawners with asynchronous breeding strategy. The attributes of G. niloticus obtained from this study reveals that the fish species is a good candidate for fish culture.

ĐA DANG DI TRUYỀN CỦA 120 GIỐNG/DÒNG ĐẬU NÀNH (Glycine max (L.) Merr.) BẰNG CHỈ THỊ PHÂN TỬ SSR

Nghiên cứu đa dạng di truyền nhằm mục đích tìm ra mối quan hệ giữa các kiểu gen trong tập đoàn giống/dòng cây trồng, từ đó có thể đưa ra chiến lược chọn tạo giống, cải thiện nguồn gen. Nghiên cứu này đã sử dụng 09 chỉ thị phân tử SSR để đánh giá mức độ đa dạng di truyền của 120 giống/dòng đậu nành (Glycine max (L.) Merr.) đang được bảo tồn tại ngân hàng giống trường Đại học Cần Thơ. Kết quả điện di sản phẩm PCR bằng 09 chỉ thị phân tử SSR thu được 52 phân đoạn và tất cả 52 phân đoạn đều có tỷ lệ đa hình trung bình cao (100%). Chỉ số PIC dao động từ 0,05 (satt596) đến 0,46 (satt009), với giá trị trung bình là 0,21. Cây phả hệ được xây dựng dựa trên 09 chỉ thị SSR bằng phân tích nhóm UPGMA phân các mẫu thành 11 nhóm chính với hệ số di truyền trung bình là 0,7 và hệ số tương đồng dao động từ 0,47 - 0,87. Kết quả này cho thấy bộ sưu tập 120 giống/dòng đậu nành rất đa dạng về bản chất di truyền và có thể dùng làm vật liệu ban đầu cho công tác chọn tạo giống đậu nành trong tương lai. ABSTRACT Genetic diversity research aims to study the relationship between genotypes in the varieties/lines, as the results, a breeding strategy will be set up for genetic improvement. In this study, 09 SSR molecular markers were used to evaluate the genetic diversity of 120 soybean varieties/lines being conserved at the gene bank of Can Tho University. A total of 52 fragments were produced by 09 SSR primers with 100% polymorphism rate. The PIC index value was ranged from 0.05 (satt596) to 0.46 (satt009), the average PIC index was 0.21. Using UPGMA analysis showed that the phylogenetic tree was divided 120 soybean varieties/lines into 11 main groups with the average genetic coefficient of 0.7 and the similarity coefficient ranging from 0.47-0.87. Thus, this result showed that the collection of 120 soybean varieties/lines is very diverse in genetic background and can be used as a starting material for future soybean breeding.

Al-Khamsa: The Prophet’s Mares - Or Were They Stallions?

Arab(ian) horse enthusiasts perpetuate an origin legend for the breed that counts five foundational mares in relation to Islamic Prophet Muhammad. Challenging both the concept of a gender preference for mares among Bedouin and/or Arab people in the early Islamic empire as well as the popular historiography of the Arab horse as a Bedouin breed promoted by Islam and in particular its prophet, this paper contextualises Al-Khamsa (the five) as evidence of matrilineal horse breeding strategy by surveying premodern Arabic material on horses.