Genetic Improvement Of Traits Research Articles

Natural variation in the chickpea metabolome under drought stress.

Chickpea is the world's fourth largest grown legume crop, which significantly contributes to food security by providing calories and dietary protein globally. However, the increased frequency of drought stress has significantly reduced chickpea production in recent years. Here, we have performed a field experiment with 36 diverse chickpea genotypes to evaluate grain yield, photosynthetic activities and molecular traits related to drought stress. For metabolomics analysis, leaf tissue was collected at three time points representing different pod-filling stages. We identified L-threonic acid, fructose and sugar alcohols involved in chickpea adaptive drought response within the mid-pod-filling stage. A stress susceptibility index for each genotype was calculated to identify tolerance capacity under drought, distributing the 36 genotypes into four categories from best to worst performance. To understand how biochemical mechanisms control different traits for genetic improvement, we performed a differential Jacobian analysis, which unveiled the interplay between various metabolic pathways across three time points, including higher flux towards inositol interconversions, glycolysis for high-performing genotypes, fumarate to malate conversion, and carbon and nitrogen metabolism perturbations. Metabolic GWAS (mGWAS) analysis uncovered gene candidates involved in glycolysis and MEP pathway corroborating with the differential biochemical Jacobian results. Accordingly, this proposed data analysis strategy bridges the gap from pure statistical association to causal biochemical relations by exploiting natural variation. Our study offers new perspectives on the genetic and metabolic understanding of drought tolerance-associated diversity in the chickpea metabolome and led to the identification of metabolic control points that can be also tested in other legume crops.

Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines.

Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.

Exploring the relationships between coagulation, composition, and hygienic quality of bulk tank milk from Manchega sheep

Milk from Manchega sheep is the raw material for the elaboration of Protected Designation of Origin (PDO) Queso Manchego, a hard-pressed cheese with one of the most established quality marks on the market worldwide. For this reason, milk quality control in this breed is one of the main targets of the dairy sheep sector. However, pricing systems still continue to apply criteria based only on milk composition and the current legislation on food hygiene. The aim of this study is to explore bulk tank sheep milk quality, estimating milk coagulation properties and their relationship with composition, somatic cell counts, and differential microbiological quality. For this purpose, 308 bulk tank milk samples were collected with seasonal periodicity, and analyses were performed for the aforementioned traits. The obtained results highlight the variability in composition, microbiology, and coagulation properties in different samples, which prevents clear relationships between milk quality parameters. However, there was evidence of a group of milk samples whose coagulation would be desirable for cheesemaking, based on values for fat, protein and total solids. Outcomes also stand out casein content as an important parameter to affect curd yield, proving the interest of using casein as trait for genetic improvement in dairy sheep breeds.

Potential of in-plant intramuscular fat predictions to enable sheep breeders to incorporate consumer preferences in breeding programmes

The inclusion of eating quality traits in sheep genetic improvement programmes is desirable. Intramuscular fat (IMF) plays a key role in ensuring consumer satisfaction when eating lamb, but genetic progress for IMF is constrained by a lack of routine data collection. This study investigated the potential for IMF predictor traits to substitute for measured IMF in genetic improvement programmes. Carcass and predicted IMF (near-infrared estimated IMF and marbling score) data were available on 10,113 New Zealand lambs, 1678 of which also had measured chemical IMF on a slice of M. longissimus lumborum on which the predictions of IMF had been made. Genetic antagonisms were observed between carcass lean traits and IMF. The genetic correlation between the predictors and measured IMF approached one, indicating that predictors of IMF can be used in genetic improvement programmes. Through using selection indexes, simultaneous increases in IMF and the existing terminal selection index are possible, provided all traits are measured. This study highlights the importance and potential of predicted IMF to achieve genetic improvement in traits of importance to consumers.

The development of effective ruminant breeding programmes in Ireland from science to practice

A genetic improvement programme is a sustainable, cumulative and permanent approach to achieving year-on-year performance gains. Its success is predicated not only on an efficient and effective breeding programme but also on a vision of the traits of importance in the future. A single, industry-owned, centralised database for cattle and sheep has been the foundation for genetic improvement programmes in Ireland. While DNA information has been heralded as a breakthrough for accelerating genetic gain, the basic principles of a successful animal breeding programme still remain the same: (1) a pertinent breeding goal, (2) the appropriate breeding objective to deliver on the breeding goal, (3) an accurate genetic evaluation system, (4) an efficient and effective breeding scheme, and (5) a system to disseminate the elite germplasm to the end user; also of importance is a system for validating the underlying procedures and principles. The constituent traits and their relative emphasis within breeding objectives will continue to be contentious. Traits that will need to be considered more in future ruminant breeding objectives include environmental impact, product quality and animal well-being, including health; while not always explicitly included in Irish breeding objectives for cattle and sheep, indirect improvements for many are expected via the genetic improvement in traits like reproductive performance and survival as well as macro measures of quality such as milk fat and protein concentration and carcass merit. Crucial for the future sustainability of ruminant production systems is the co-evolution of management systems and breeding programmes so that the animal of the future is suited to the most sustainably efficient production system.

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)

BackgroundNumerous quantitative trait loci (QTLs) and candidate genes associated with yield-related traits have been identified in cotton by genome-wide association study (GWAS) analysis. However, most of the phenotypic data were from a single or few environments, and the stable loci remained to be validated under multiple field environments.ResultsHere, 242 upland cotton accessions collected from different origins were continuously investigated for phenotypic data of four main yield components, including boll weight (BW) and lint percentage (LP) under 13 field environments, and boll number per plant (BN) and seed index (SI) under 11 environments. Correlation analysis revealed a positive correlation between BN and LP, BW and SI, while SI had a negative correlation with LP and BN. Genetic analysis indicated that LP had the highest heritability estimates of 94.97%, followed by 92.08% for SI, 86.09% for BW, and 72.92% for BN, indicating LP and SI were more suitable traits for genetic improvement. Based on 56,010 high-quality single nucleotide polymorphisms (SNPs) and GWAS analysis, a total of 95 non-redundant QTLs were identified, including 12 of BN, 23 of BW, 45 of LP, and 33 of SI, respectively. Of them, 10 pairs of homologous QTLs were detected between A and D sub-genomes. We also found that 15 co-located QTLs with more than two traits and 12 high-confidence QTLs were detected under more than six environments, respectively. Further, two NET genes (GH_A08G0716 and GH_A08G0783), located in a novel QTL hotspot (qtl24, qtl25 and qlt26) were predominately expressed in early fiber development stages, exhibited significant correlation with LP and SI. The GH_A07G1389 in the stable qtl19 region encoded a tetratricopeptide repeat (TPR)-like superfamily protein and was a homologous gene involved in short fiber mutant ligon lintless-y (Liy), implying important roles in cotton yield.ConclusionsThe present study provides a foundation for understanding the regulatory mechanisms of yield components and may enhance yield improvement through molecular breeding in cotton.

Diversity for morphological traits, flowering time and leaf isoflavone content among ecotypes of

Trifolium subterraneum L. subsp. yanninicum is a pasture legume that is widely grown in medium and high rainfall areas of southern Australia and shows waterlogging tolerance. This study investigated diversity within subsp. yanninicum corresponding to eco-geographic variables, which may help to identify adapted parents with new traits for genetic improvement. Diversity for 10 morphological traits, flowering time and leaf isoflavone content was investigated using 108 ecotypes derived from wild Mediterranean populations and 10 cultivars, grown as spaced plants. Among the ecotypes, the range of flowering time was 94–149 days after sowing, and contents of formononetin, genistein and biochanin A were 0.05–1.38%, 0.73–2.33% and 0.15–2.10% of dry matter, respectively. Leaf markings also varied considerably. Leaf size and petiole length were correlated at each growth stage. Later flowering genotypes had larger leaves, longer petioles, longer internodes and thicker stems at flowering, but smaller leaves and shorter petioles at both 63 and 88 days after sowing. Contents of genistein and biochanin A were unrelated, but both were negatively associated with formononetin. Flowering time had a weak positive influence on genistein and biochanin A, but a weak negative influence on formononetin. All traits among the ecotypes (except stem diameter and leaf mark crescent size) were significantly correlated with at least one of 22 eco-geographic variables from their collection sites. Precipitation and altitude were more influential than temperature. The study found sufficient diversity to broaden the narrow genetic base of current subsp. yanninicum cultivars; however, other agronomically important traits also need to be considered. Further diversity may result from targeted collection, particularly in areas not represented in annual legume genebanks.

Evaluation of Turkish Maize Landraces Through Observing Their Yield and Agro-Morphological Traits for Genetic Improvement of New Maize Cultivars

Evaluation of Turkish Maize Landraces Through Observing Their Yield and Agro-Morphological Traits for Genetic Improvement of New Maize Cultivars

Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

BackgroundChloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast’ variation pattern of poplar at the single-base level during the transmission from mother to offspring remains unknown.ResultsHere, we constructed high-quality and almost complete chloroplast genomes for three poplar clones, ‘NL895’ and its parents, ‘I69’ and ‘I45’, from the short-read datasets using multi-pass sequencing (15–16 times per clone) and ultra-high coverage (at least 8500× per clone), with the four-step strategy of Simulation–Assembly–Merging–Correction. Each of the three resulting chloroplast assemblies contained contigs covering > 99% of Populus trichocarpa chloroplast DNA as a reference. A total of 401 variant loci were identified by a hybrid strategy of genome comparison-based and mapping-based single nucleotide polymorphism calling. The genotypes of 94 variant loci were different among the three poplar clones. However, only 1 of the 94 loci was a missense mutation, which was located in the exon region of rpoC1 encoding the β’ subunit of plastid-encoded RNA polymerase. The genotype of the loci in NL895 and its female parent (I69) was different from that of its male parent (I45).ConclusionsThis research provides resources for further chloroplast genomic studies of a F1 full-sibling family derived from a cross between I69 and I45, and will improve the application of chloroplast genomic information in modern Populus breeding programs.

Targeted Genome Editing in Genes and cis-Regulatory Regions Improves Qualitative and Quantitative Traits in Crops

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (CRISPR/Cas9)-based genome-editing system is a revolutionary technology for targeted mutagenesis in molecular biology research and genetic improvement of traits in crops (Cong et al., 2013; Ma et al., 2015, 2016). Agronomic traits of crops are controlled by major genes and quantitative trait loci (QTL). Therefore, the CRISPR/Cas9 system can be used to effectively and rapidly produce mutant traits by different strategies (Figure 1A–1C).

Variations in physiological traits as screening tool for drought tolerance in barley (Hordeum vulgare L.)

The utilization of physiological traits in genetic improvement of drought tolerance in barley (Hordeum vulgare L.) requires establishment of significant association between grain yield and the physiological traits and their genetic variations. The study was aimed at to determine variability in yield-attributes, yield and physiological traits in advance F6 lines and commercial varieties of barley, and to establish the relationship among these characters in irrigated (2 irrigations at 40 and 80 days after sowing) and rainfed (no post sowing irrigation) conditions. Yield attributes, yield and physiological traits decreased significantly in rainfed than irrigated condition. Biomass was positively and significantly associated (R2 = 0.82, P < 0.001) with grain yield. Rates of photosynthesis (Pn) of flag leaf were positively related to biomass (R2 = 0.68, P < 0.001) and grain yield (R2 = 0.52, P < 0.01). Midday (1200–1400 h) leaf relative water content (RWC) showed strong association with Pn (R2 = 0.90, P < 0.001) and biomass (R2 = 0.65, P < 0.001). Since, RWC being a simple and inexpensive trait to measure, showing strong association with Pn and biomass, which determined grain yield, could be employed as a tool to screen barley genotypes for drought tolerance.

Phenotypic characterization of indigenous rice (Oryza sativa L.) germplasm collected from the state of Nagaland, India

Nagaland is one of the eight states in the north-eastern region of India, where a considerable diversity exists in cultivated rice. Recent exploration in this tribal-dominated state has resulted in a collection of 130 rice accessions growing under diverse agroecological conditions. The agromorphological characterization data of 124 rice landraces revealed a significant variability in plant architecture and grain morphological and quality traits. Multivariate analyses including principal component analysis (PCA) and cluster analysis were performed to assess the patterns of morphological variation. The PCA extracted 12 components, which explained 75.4% of the total variation for 38 quantitative and qualitative traits. The cluster analysis grouped 124 rice landraces into five clusters, and the number of landraces in each cluster ranged from 1 to 59. The correlations among the traits are discussed, which will be useful in considering traits for genetic improvement in grain yield and quality. The landraces have been conserved in the national genebank for further utilization.

Calving day and age at first calving in Angus heifers1

Because of difficulties in data collection and analysis, in most breeds there have been limited ways to evaluate fertility in females on a between-herd basis. The objective of this study was to determine the heritabilities (direct and maternal) for CD (calving day) and AFC (age at first calving) in American Angus heifers and to evaluate the potential for using these traits in genetic improvement of female fertility. Records (n = 2,082) from 2 herds were used. Calving day was defined as the calving date of a heifer minus the first calving date in her contemporary group. To avoid bias, noncalving heifers were assigned a penalty record CD of 30, 60, and 90 d after the last CD in that contemporary group. These assigned CD were also used to give open heifers a predicted AFC. Data were analyzed by MTDFREML using a general linear animal model. Fixed effects included herd-year, service sire of the heifer, and age of dam, and a covariate of age of the heifer at the start of the breeding season (for CD only). A model including a maternal effect was also analyzed. Heritabilities for CD using a direct model were 0.07 +/- 0.04, 0.10 +/- 0.05, and 0.11 +/- 0.05, for each penalty adjustment, respectively. Average, minimum, and maximum estimated breeding values (in days) for sires of heifers for the 3 adjustments were -0.7, -10.6, and 9.8; -1.1, -17.2, and 16.5; and -1.6, -22.6, and 19.5. The estimates of heritability for AFC using a direct model did not differ for the different adjustments for penalty records and were 0.28 +/- 0.06. Average, minimum, and maximum estimated breeding values (in days) for sires of heifers for the 3 adjustments were -0.6, -46.6, and 45.9; -1.2, -50.1, and 51.6; and -1.7, -52.9, and 56.7. In a direct-maternal model, direct heritabilities for CD decreased slightly, and for AFC increased to 0.66 +/- 0.14. The maternal heritabilities and direct-maternal genetic correlations were 0.08 +/- 0.05 and -0.18 +/- 0.58 for CD, and 0.32 +/- 0.08 and -0.85 +/- 0.06 for AFC. Although AFC had a greater heritability and a wider range of breeding values than CD, the negative direct-maternal genetic correlation indicated that selecting on AFC may favor heifers that are themselves born later in the season. Therefore, CD may be more useful than AFC in selecting for female fertility in beef cattle.

Evaluation of Bonsmara and Belmont Red cattle breeds in South Africa. 2. Genetic parameters for growth and fertility

Genetic parameters were estimated for growth and fertility indicator traits in a South African beef cattle population. Measurements on 5601 pedigreed progeny of 96 Bonsmara sires, 18 Belmont Red sires and 20 Bonsmara × Belmont Red cross sires were recorded over 19 years in 4 diverse climatic regions of South Africa. Growth traits were measured on growing stock from birth to 18 months at pasture. Cow weights were measured at calving and weaning. Age at first calving, and repeated measurements of calving day and calving interval were recorded on 1993 breeding females as indicators of reproductive performance. The traits were analysed using univariate and bivariate animal models with maternal effects fitted. Direct heritability of growth traits (0.11–0.42) and female fertility traits (0.02–0.13) suggested that genetic progress could be made by selection for some traits. Genetic correlations between growth and fertility traits were variable (–0.47–0.85) and indicated that multi-trait selection would be the best method of dealing with multidirectional forces on productivity traits. Genetic correlations between direct and maternal effects on liveweight traits were mostly negative indicating that genetic improvement of traits with strong maternal influence, such as weaning weight, would be complicated and supported the use of post-weaning weights with less maternal influence as selection criteria to improve the direct additive component of growth. The genetic parameter estimates provide useful reference values for estimation of breeding values in a proposed combined-breed genetic evaluation program.

Opportunities for detection and use of QTL influencing seasonal reproduction in sheep: a review

Genetic improvement in traits associated with seasonal breeding in sheep is challenging because these traits have low heritabilities, are generally not expressed until late in life, are commonly recorded only in females, and are expressed only in some lambing seasons and management systems. Detection of quantitative trait loci and their use in marker-assisted selection could therefore substantially enhance selection responses. A population of sheep with an extended breeding season was developed through selection for fertility in spring matings and provides opportunities for further study of candidate genes influencing seasonal breeding. In particular, the melatonin receptor 1a gene is polymorphic in many sheep breeds and appears to influence a number of seasonal reproductive responses. In addition, a variety of clock genes have been identified in laboratory mammals and shown to influence biological rhythms. Mutations in these clock genes have been identified and shown to influence circadian periodicities and reproductive patterns in golden hamster and mouse. In sheep, expression of clock genes in the suprachaismatic nucleus and pars tuberalis (PT) suggests that "calendar" cells in the ovine PT play a role in maintaining circannual rhythms. Thus the various clock genes represent potentially important candidate genes that may be involved in control of seasonal breeding.

Opportunities for detection and use of QTL influencing seasonal reproduction in sheep: a review

Genetic improvement in traits associated with seasonal breeding in sheep is challenging because these traits have low heritabilities, are generally not expressed until late in life, are commonly recorded only in females, and are expressed only in some lambing seasons and management systems. Detection of quantitative trait loci and their use in marker-assisted selection could therefore substantially enhance selection responses. A population of sheep with an extended breeding season was developed through selection for fertility in spring matings and provides opportunities for further study of candidate genes influencing seasonal breeding. In particular, the melatonin receptor 1a gene is polymorphic in many sheep breeds and appears to influence a number of seasonal reproductive responses. In addition, a variety of clock genes have been identified in laboratory mammals and shown to influence biological rhythms. Mutations in these clock genes have been identified and shown to influence circadian periodicities and reproductive patterns in golden hamster and mouse. In sheep, expression of clock genes in the suprachaismatic nucleus and pars tuberalis (PT) suggests that "calendar" cells in the ovine PT play a role in maintaining circannual rhythms. Thus the various clock genes represent potentially important candidate genes that may be involved in control of seasonal breeding.

Estimation of genetic variation in plasma leptin concentrations in pre-pubertal heifers

Leptin is involved in the regulation of food intake, energy expenditure and whole body energy balance. In livestock species these processes are important for optimisation of growth, reproduction, lactation and overall health and well-being. Condition score is a useful indicator of energy balance and is highly correlated (-0.84) genetically to commencement of luteal activity (CLA), an endocrine measurement of fertility in dairy cattle (Royal et al., submitted). Circulating leptin levels drop post-partum reflecting changes in energy balance and fat mobilisation. The interval to first ovulation post-partum is phenotypically correlated (0.83) to the interval from parturition to the leptin nadir (Kadokawa et al. 2000), suggesting that a delay in the recovery of leptin secretion postpartum increases the delay to first ovulation. The heritability of circulating leptin concentrations in humans and pigs is high (0.39-0.61; Cameron et al., 2000; Rotimi et al., 1997). If this were also the case in cattle, and postpartum changes were related to concentrations at an early age, then it would be of immense value to the genetic improvement of traits associated with fertility.

PIG BREEDING: CURRENT PROGRAMS VS. FUTURE PRODUCTION REQUIREMENTS

Reports reported annually for the Canadian ROP swine testing program provide no evidence of genetic trends in the seed stock herds enrolled. Small herd size (&lt; 8 sows), short average life span of these herds (&lt; 5 yr) and the geographically diffuse nature of the seed stock industry appear to have been major impediments to the application of cohesive and sustained selection programs. The commercial industry, in contrast, has shown a marked improvement in average carcass merit during the past decade. This trend, stimulated and guided by the 1968 revision of carcass grading standards, has been accompanied by a 60% reduction in the number of commercial herds and a three-fold increase in the average number of pigs marketed annually per unit. The specific breeding programs employed by the commercial industry cannot be documented but there has been a steady growth in the use of systematic crossbreeding programs, and producer demand for boars with performance credentials has greatly intensified. This has fostered a fivefold increase in ROP testing activity since 1973, given impetus to the evolution of swine AI programs, and encouraged the development of large closed-herd seed stock operations with self-contained performance test facilities. The central objective of performance testing programs, both private and public, is the genetic improvement of traits directly relevant to efficient lean meat production. Future production requirements are unlikely to alter this basic objective but advances in the technology for live animal carcass evaluation and changing economic circumstances, specifically changes in rations to accommodate the increasing competition for cereal grain supplies, will necessitate continuous review and revision of testing procedures. Recent experimental evidence indicates that rate of feed ingestion is inversely related to efficiency of digestion and lean tissue feed conversion. This implies that testing programs which place a premium on rate of ingestion (e.g. "to appetite" or "scale" feeding) may be less suitable for purposes of measuring genetic differences in efficiency of lean production than programs which utilize ad libitum feeding.