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Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches

Haque MA, Rafii MY, Yusoff MM, Ali NS, Yusuff O, Arolu F, et al.

Mol Biol Rep, 2023 Mar;50(3):2795-2812.
PMID: 36592290 DOI: 10.1007/s11033-022-07853-9

Natural and man-made ecosystems worldwide are subjected to flooding, which is a form of environmental stress. Genetic variability in the plant response to flooding involves variations in metabolism, architecture, and elongation development that are related with a low oxygen escape strategy and an opposing quiescence scheme that enables prolonged submergence endurance. Flooding is typically associated with a decrease in O2 in the cells, which is especially severe when photosynthesis is absent or limited, leading to significant annual yield losses globally. Over the past two decades, considerable advancements have been made in understanding of mechanisms of rice adaptation and tolerance to flooding/submergence. The mapping and identification of Sub1 QTL have led to the development of marker-assisted selection (MAS) breeding approach to improve flooding-tolerant rice varieties in submergence-prone ecosystems. The Sub1 incorporated in rice varieties showed tolerance during flash flood, but not during stagnant conditions. Hence, gene pyramiding techniques can be applied to combine/stack multiple resistant genes for developing flood-resilient rice varieties for different types of flooding stresses. This review contains an update on the latest advances in understanding the molecular mechanisms, metabolic adaptions, and genetic factors governing rice flooding tolerance. A better understanding of molecular genetics and adaptation mechanisms that enhance flood-tolerant varieties under different flooding regimes was also discussed.

Matched MeSH terms: Selective Breeding
Fulltext Assessment of Oil Palm Pollinating Weevil (Elaeidobius kamerunicus) Population Density in Biparental dura × pisifera Hybrids on Deep Peat-Soil in Perak State, Malaysia

Swaray S, Y Rafii M, Din Amiruddin M, Firdaus Ismail M, Jamian S, Jalloh M, et al.

Insects, 2021 Mar 04;12(3).
PMID: 33806613 DOI: 10.3390/insects12030221

This study was conducted to assess the Elaeidobius kamerunicus (EK) population density among the biparental dura × pisifera hybrids' palms on deep peat-soil. Twenty-four hybrids derived from 10 genetic sources were used. Variance analysis showed that the EK population density varies between different oil palm hybrids, with a more noticeable variation of a low population mean in the male weevil across the hybrids. The highest weevil population mean/spikelet was attained on the third day of anthesis. The maximum monthly population of EK/spikelet (12.81 ± 0.23) and population density of EK (1846.49 ± 60.69) were recorded in January. Accordingly, 41.67% of the hybrids recorded an EK population density greater than the trial means of 973.68 weevils. Hybrid ECPHP550 had the highest mean of EK/spikelet (10.25 ± 0.11) and the highest population density of EK/palm (1241.39 ± 73.74). The parental mean population was 963.24 weevils and parent Deli-Banting × AVROS recorded the highest EK population density (1173.01). The overall results showed a notable disparity in the EK population among the biparental hybrids. Parental Deli-Banting × AVROS and hybrid ECPHP550 could be more useful to optimize the weevil population for pollination improvements in palm plantations. However, we suggest that volatile production should be included as a desirable trait in oil palm selective breeding.

Matched MeSH terms: Selective Breeding
Fulltext The Effects of Feed Restriction and Isolated or Group Rearing on the Measurement of Individual Feed Intake and Estimation of Feed Conversion Ratio in Juvenile Nile Tilapia (Oreochromis niloticus) for Selective Breeding Purposes

Rodde C, Vandeputte M, Trinh TQ, Douchet V, Canonne M, Benzie JAH, et al.

Front Genet, 2020;11:596521.
PMID: 33519898 DOI: 10.3389/fgene.2020.596521

Accurately measuring the phenotype at the individual level is critical to the success of selective breeding programs. Feed efficiency is a key sustainability trait and is typically approached through feed conversion ratio (FCR). This requires measurements of body weight gain (BWG) and feed intake (FI), the latter being technically challenging in fish. We assessed two of the principal methods for measuring feed intake in fish over consecutive days: (1) group rearing 10 fish per group and video recording the meals and (2) rearing fish individually on a restricted ration. Juvenile Nile tilapia (Oreochromis niloticus) from the Genetically Improved Farmed Tilapia (GIFT) strain and the Cirad strain were entered into the study (128 GIFT and 109 Cirad). The GIFT strain were reared over three consecutive periods of 7 days each under different feeding, recording, and rearing scenarios (i) in groups fed an optimal ration (g100) or (ii) fed a 50% restricted ration (g50) both with video records of all meals and (iii) reared in isolation and fed a 50% restrictive ration. The Cirad strain were tested similarly but only for scenarios (i) and (iii). All fish were fed twice daily with a calculated ration. Correlations showed the same trends for the GIFT and the Cirad strains. For the GIFT strain, correlations were positive and significant for BWG and FI measured in scenarios (i) and (ii), 0.49 and 0.63, respectively, and FI measured in scenarios (i) and (iii) (0.50) but not for BWG measured in scenarios (i) and (iii) (0.29, NS). The phenotypic correlation estimated for FCR between scenarios (i) and (ii) with fish fed an optimal or a 50% restricted ration was low and not significant (0.22). Feed Conversion Ratio for GIFT fish reared in groups or in isolation and fed with a restricted ration [scenarios (ii) and (iii)] were not significantly correlated either. Social interactions between fish, potentially impacting their efficiency, may explain the results. Therefore, selective breeding programs seeking to improve feed efficiency will need to carefully plan the feeding rate and the rearing system used to estimate FCR in order to optimize selection for the targeted production system.

Matched MeSH terms: Selective Breeding
Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus

Lind CE, Kilian A, Benzie JAH

Anim. Genet., 2017 Jun;48(3):362-364.
PMID: 28094451 DOI: 10.1111/age.12536

The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.

Matched MeSH terms: Selective Breeding
Selection of high yielding Jatropha curcas L. accessions for elite hybrid seed production

Nurul Hidayah Che Mat, Md Atiqur Rahman Bhuiyan, Senan S, Ratnam W, Zahira Yaakob

Sains Malaysiana, 2015;44:1567-1572.

Phenotypic selection of individuals is the first step in a selective breeding program for elite hybrid seed production. In
this study, a total of 295 Jatropha curcas individuals raised from cuttings representing 21 accessions, collected from eight
different countries were evaluated for growth performance. The evaluation was done at the Biodiesel Research Station
of Universiti Kebangsaan Malaysia, Kuala Pilah from December 2012 to December 2013. Individual plants from each
accession were observed on several agronomic and yield related traits and all the data were recorded periodically.
Performance of each accession was analyzed using Statistical Analysis System (SAS) 9.4. Four traits which were plant
height (PH), number of flowers per inflorescence (NFI), number of female flowers per inflorescence (NFFPI) and hundred
seed weight (HSW) showed significant differences among the accessions after one year of planting. Maximum values for
each trait were 115.5 cm for PH, 6 for number of branches per plant (BPP), 9 for number of inflorescences per plant
(NIPP), 25 for number of fruits per plant (NFPP), 5 for number of fruits per inflorescence (NFPI), 191 for NFI, 10 for
NFFPI, 81.0 g for HSW and 70 for number of seeds per plant (NSPP). Accession number 1 from Thailand showed the best
performance for most traits. A highly significant and positive correlation was found between NFPP and NSPP. Based on
superior trait values for NIPP, NFPP, NFPI, NFI, NFFPI and HSW, five plants from accession UKMJC 01, 04, 05, 13 and 14
have been selected for generating elite intraspecific hybrids.

Matched MeSH terms: Selective Breeding
Fulltext Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus

de Verdal H, Vandeputte M, Mekkawy W, Chatain B, Benzie JAH

BMC Genet, 2018 11 16;19(1):105.
PMID: 30445908 DOI: 10.1186/s12863-018-0691-y

BACKGROUND: Improving feed efficiency in fish is crucial at the economic, social and environmental levels with respect to developing a more sustainable aquaculture. The important contribution of genetic improvement to achieve this goal has been hampered by the lack of accurate basic information on the genetic parameters of feed efficiency in fish. We used video assessment of feed intake on individual fish reared in groups to estimate the genetic parameters of six growth traits, feed intake, feed conversion ratio (FCR) and residual feed intake in 40 pedigreed families of the GIFT strain of Nile tilapia, Oreochromis niloticus. Feed intake and growth were measured on juvenile fish (22.4 g mean body weight) during 13 consecutive meals, representing 7 days of measurements. We used these data to estimate the FCR response to different selection criteria to assess the potential of genetics as a means of increasing FCR in tilapia.
RESULTS: Our results demonstrate genetic control for FCR in tilapia, with a heritability estimate of 0.32 ± 0.11. Response to selection estimates showed FCR could be efficiently improved by selective breeding. Due to low genetic correlations, selection for growth traits would not improve FCR. However, weight loss at fasting has a high genetic correlation with FCR (0.80 ± 0.25) and a moderate heritability (0.23), and could be an easy to measure and efficient criterion to improve FCR by selective breeding in tilapia.
CONCLUSION: At this age, FCR is genetically determined in Nile tilapia. A selective breeding program could be possible and could help enabling the development of a more sustainable aquaculture production.

Matched MeSH terms: Selective Breeding/genetics
Genetic diversity analysis in Malaysian giant prawns using expressed sequence tag microsatellite markers for stock improvement program

Atin KH, Christianus A, Fatin N, Lutas AC, Shabanimofrad M, Subha B

Genet. Mol. Res., 2017 Aug 17;16(3).
PMID: 28829885 DOI: 10.4238/gmr16035685

The Malaysian giant prawn is among the most commonly cultured species of the genus Macrobrachium. Stocks of giant prawns from four rivers in Peninsular Malaysia have been used for aquaculture over the past 25 years, which has led to repeated harvesting, restocking, and transplantation between rivers. Consequently, a stock improvement program is now important to avoid the depletion of wild stocks and the loss of genetic diversity. However, the success of such an improvement program depends on our knowledge of the genetic variation of these base populations. The aim of the current study was to estimate genetic variation and differentiation of these riverine sources using novel expressed sequence tag-microsatellite (EST-SSR) markers, which not only are informative on genetic diversity but also provide information on immune and metabolic traits. Our findings indicated that the tested stocks have inbreeding depression due to a significant deficiency in heterozygotes, and FIS was estimated as 0.15538 to 0.31938. An F-statistics analysis suggested that the stocks are composed of one large panmictic population. Among the four locations, stocks from Johor, in the southern region of the peninsular, showed higher allelic and genetic diversity than the other stocks. To overcome inbreeding problems, the Johor population could be used as a base population in a stock improvement program by crossing to the other populations. The study demonstrated that EST-SSR markers can be incorporated in future marker assisted breeding to aid the proper management of the stocks by breeders and stakeholders in Malaysia.

Matched MeSH terms: Selective Breeding
Fulltext Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia (Oreochromis niloticus) in Egypt

Nayfa MG, Jones DB, Benzie JAH, Jerry DR, Zenger KR

Front Genet, 2020;11:567969.
PMID: 33193660 DOI: 10.3389/fgene.2020.567969

Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9-11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.

Matched MeSH terms: Selective Breeding
Fulltext Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, et al.

Science, 2020 06 26;368(6498):1495-1499.
PMID: 32587022 DOI: 10.1126/science.aaz8599

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

Matched MeSH terms: Selective Breeding
Fulltext Genes and genealogy of the guppy fish, Poecilia reticulata

Khoo, Gideon, Lim, Tit Meng, Phang, Violet Pan Eng

Buletin Persatuan Genetik Malaysia, 2006;12(1):5-7.
MyJurnal

Since the early 1950’s, Singapore is internationally known as the guppy-breeding centre. At least 40 different colour varieties of guppies are cultured in Singapore, with each farm specialising in 10 to 15 varieties. These fancy varieties have been developed by skilful farmers through intensive and continual selective breeding. Genes controlling background body pigmentation such as albino (a), blond (b), gold (g) and blue (r) are autosomally inherited and recessive to their wild-type alleles which produce drab olive-brown background coloration. Colour patterns which are superimposed onto wild-type background coloration are due to genes located on the sex chromosomes. These
sex-linked colour genes are dominant and sex-limited to males as their expression requires male hormones. Y-linked colour pattern genes carried by males are inherited only along the paternal line while X-linked genes are present in both sexes. Among the guppy varieties produced locally, only two Y-linked genes, Ssb and Sst, that control snakeskin tail and body patterns, respectively, have been found in varieties with snakeskin-like reticulations. Single colour genes that are both X- and Y-linked produce red (Rdt), blue (Blt), green (Grt), black (Bt) and variegated (Var) patterns
on the caudal fin. The black caudal-peduncle of the Tuxedo variety is the result of Bcp, a gene that is both X- and Ylinked. Different combinations of colour pattern genes and background pigmentation genes as well as interactions among them give rise to various colour phenotypes. For
instance, the inclusion of Bcp in Snakeskin varieties causes black reticulations on the tail fin to be replaced by large, coarse black spots. Neon coloration is produced by interactions between the Ln (light turquoise) gene with Blt, Rdt and Bcp.

Matched MeSH terms: Selective Breeding

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