Association Analysis of Simple Sequence Repeat (SSR) Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb.)

Adaptive strategies to drought stress in grasses of the poaceae family under climate change: Physiological, genetic and molecular perspectives: A review

Drought stress is one of the most critical abiotic factors which negatively impacts on growth, productivity, and survival of plants. Grass species have an important role in the sustainable intensification of cropping systems. This review focus on the specific drought tolerance characteristics in grass species and application of prevalent classical and molecular methods for genetic improvement of them to drought stress. Generally, grass species adapt to drought stress by utilizing more than one strategy including of changes in the root growth, photosynthetic pigments, activation of antioxidant enzymes, and accumulation of compatible osmolytes. They also have other specific characteristics consisted of summer dormancy, drought recovery, and persistence, which lead to drought adaptation after prolonged drought. Studies on different grasses, indicated that most of above mentioned traits usually have positive correlation with drought tolerance. Also, high heritability has been reported for most of them in different grasses. Therefore, an effective index might be considering in identification of drought tolerance genotypes. Recently, high-throughput imaging phenotyping and advanced molecular techniques such as genotyping-by-sequencing (GBS), RNA sequencing, genome-wide association study, and genome editing help conventional breeding methods to increase the accuracy, selection efficiency, genetic gains, and speed of breeding programs for developing drought tolerant cultivars.

Root system architecture and genomic plasticity to salinity provide insights into salt-tolerant traits in tall fescue

Salinity is detrimental to soil health, plant growth, and crop productivity. Understanding salt tolerance mechanisms offers the potential to introduce superior crops, especially in coastal regions. Root system architecture (RSA) plasticity is vital for plant salt stress adaptation. Tall fescue is a promising forage grass in saline regions with scarce RSA studies. Here, we used the computer-integrated and -automated programs EZ-Rhizo II and ROOT-Vis II to analyze and identify natural RSA variations and adaptability to high salt stress at physiological and genetic levels in 17 global tall fescue accessions. Total root length rather than the number of lateral roots contribute more to water uptake and could be used to separate salt-tolerant (LS-11) and -sensitive accessions (PI531230). Comparative evaluation of LS-11 and PI531230 demonstrated that the lateral root length rather than the main root contributed more towards the total root length in LS-11. Also, high water uptake was associated with a larger lateral root vector and position while low water intake was associated with an insignificant correlation between root length, vector, and position. To examine candidate gene expression, we performed transcriptome and transcription analyses using high-throughput RNA sequencing and real-time quantitative PCR, respectively of the lateral and main roots. The main root displayed more differentially expressed genes than the lateral root. A Poisson comparison of LS-11 vs PI531230 demonstrated significant upregulation of PLASMA MEMBRANE AQUAPORIN 1 and AUXIN RESPONSE FACTOR 22 in both the main and lateral root, which are associated with transmembrane water transport and the auxin-activated signaling system, respectively. There is also an upregulation of BASIC HELIX-LOOP-HELIX 5 in the main root and a downregulation in the lateral root, which is ascribed to sodium ion transmembrane transport, as well as an upregulation of THE MEDIATOR COMPLEX 1 assigned to water transport in the lateral root and a downregulation in the main root. Gene-protein interaction analysis found that more genes interacting with aquaporins proteins were upregulated in the lateral root than in the main root. We inferred that deeper main roots with longer lateral roots emanating from the bottom of the main root were ideal for tall fescue water uptake and salt tolerance, rather than many shallow roots, and that, while both main lateral roots may play similar roles in salt sensing and water uptake, there are intrinsic genomic differences.

Association analysis revealed loci linked to post-drought recovery and traits related to persistence of smooth bromegrass (Bromus inermis)

Association analysis has been proven as a powerful tool for the genetic dissection of complex traits. This study was conducted to identify association of recovery, persistence, and summer dormancy with sequence related amplified polymorphism (SRAP) markers in 36 smooth bromegrass genotypes under two moisture conditions and find stable associations. In this study, a diverse panel of polycross-derived progenies of smooth bromegrass was phenotyped under normal and water deficit regimes for three consecutive years. Under water deficit, dry matter yield of cut 1 was approximately reduced by 36, 39, and 37% during 2013, 2014, and 2015, respectively, compared with the normal regime. For dry matter yield of cut 2, these reductions were approximately 38, 60, and 56% in the same three consecutive years relative to normal regime. Moreover, water deficit decreased the RY and PER of the genotypes by 35 and 28%, respectively. Thirty primer combinations were screened by polymerase chain reaction (PCR). From these, 541 polymorphic bands were developed and subjected to association analysis using the mixed linear model (MLM). Population structure analysis identified five main subpopulations possessing significant genetic differences. Association analysis identified 69 and 46 marker-trait associations under normal and water deficit regimes, respectively. Some of these markers were associated with more than one trait; which can be attributed to pleiotropic effects or tightly linked genes affecting several traits. In normal and water-deficit regimes, these markers could potentially be incorporated into marker-assisted selection and targeted trait introgression for the improvement of drought tolerance of smooth bromegrass.

Protein patterns and their association with photosynthetic pigment content, agronomic behavior, and origin of purslane accessions (Portulaca oleracea L.)

In this study, the proteomic, morphometric, and photosynthetic pigment data of purslane (Portulaca oleracea) accessions were combined together to show their impact on genetic variation in order to establish a relationship between protein patterns and phenotypic behavior of the plant. Seeds of 18 collected purslane accessions were cultivated based on a completely randomized design with three replicates. Before the flowering stage, the data on morphology, photosynthetic pigment content, and seed proteins were obtained. The results showed a significant difference among purslane accessions in terms of the most studied agronomic characteristics and the content of photosynthetic pigments and proteins. The cluster analysis of the 18 purslane accessions based on agronomic data, and photosynthetic pigment content, and protein pattern data produced three main clusters. Moreover, the seed protein analysis revealed that the two polymorphic protein bands of size 40 kDa (protein "a") and 30 kDa (protein "b") effectively diversified the agronomic, photosynthetic pigment, and phylogenetic relationships among the purslane accessions. Interestingly, protein "a" was produced in plants growing in low altitude areas and played a suppressive role for TDW, while protein "b" was produced in plants growing in high altitude areas and functioned as an activator agent for this trait. Overall, the outcomes of the present study indicated the presence of high genetic variability (77.6%) among the purslane accessions. These findings suggest that these proteins should be sequenced for further proteomic analyses and can be used for hybridization to generate useful recombinants in segregating generations and improve breeding varieties of P. oleracea.

Marker-trait association analysis for drought tolerance in smooth bromegrass

BACKGROUND

Little information is available on the application of marker-trait association (MTA) analysis for traits related to drought tolerance in smooth bromegrass. The objectives of this study were to identify marker loci associated with important agronomic traits and drought tolerance indices as well as fining stable associations in a diverse panel of polycross derived genotypes of smooth bromegrass. Phenotypic evaluations were performed at two irrigation regimes (normal and deficit irrigation) during 2 years; and association analysis was done with 626 SRAP markers.

RESULTS

The results of population structure analysis identified three main subpopulations possessing significant genetic differences. Under normal irrigation, 68 and 57 marker-trait associations were identified using general linear model (GLM) and mixed linear mode1 (MLM), respectively. While under deficit irrigation, 61 and 54 markers were associated with the genes controlling the studied traits, based on these two models, respectively. Some of the markers were associated with more than one trait. It was revealed that markers Me1/Em5-11, Me1/Em3-15, and Me5/Em4-7 were consistently linked with drought-tolerance indices.

CONCLUSION

Following marker validation, the MTAs reported in this panel could be useful tools to initiate marker-assisted selection (MAS) and targeted trait introgression of smooth bromegrass under normal and deficit irrigation regimes, and possibly fine mapping and cloning of the underlying genes and QTLs.

Insights into nitrogen fixing traits and population structure analyses in cowpea (Vigna unguiculata L. Walp) accessions grown in Ghana

With legumes, symbiotic N₂ fixation can meet the species N demand and reduce the over-reliance on chemical fertilizers in tropical regions where N deficiency is a major factor limiting crop yields and increased agricultural sustainability. Therefore, to optimize the use of cowpea (Vigna unguiculata L. Walp) germplasm in effective breeding, evaluation of genetic diversity and quantification of N₂ fixation are essential prerequisites. The aim of this study was to explore the level of diversity using SSR markers and N₂-fixing traits in a set of cowpea germplasm grown in Ghana. We analysed 49 cowpea accessions collected from Northern Ghana using qualitative vegetative and N₂ fixation traits, and simple sequence repeat (SSR) markers. Experimental field results revealed considerable morpho-physiological variation for plant growth habits, grain yield and symbiotic performance between and among the cowpea accessions. Results from both the ¹⁵N natural abundance and ureides in the xylem sap were able to descriminate between high and low levels of N₂ fixation in cowpea accessions. Five subpopulations were identified within accessions inferred from STRUCTURE 2.3.4. A general linear model was used to assess the association of SSR markers with N₂-fixing traits. There were significant (p ≤ 0.05) links between SSR markers and symbiosis-related traits such as nodule number, nodule dry weight, shoot dry weight, N-fixed, N derived from air (Ndfa), and relative uried-N (RU-N).

Association mapping unveils favorable alleles for grain iron and zinc concentrations in lentil (Lens culinaris subsp. culinaris)

Lentil is a major cool-season grain legume grown in South Asia, West Asia, and North Africa. Populations in developing countries of these regions have micronutrient deficiencies; therefore, breeding programs should focus more on improving the micronutrient content of food. In the present study, a set of 96 diverse germplasm lines were evaluated at three different locations in India to examine the variation in iron (Fe) and zinc (Zn) concentration and identify simple sequence repeat (SSR) markers that associate with the genetic variation. The genetic variation among genotypes of the association mapping (AM) panel was characterized using a genetic distance-based and a general model-based clustering method. The model-based analysis identified six subpopulations, which satisfactorily explained the genetic structure of the AM panel. AM analysis identified three SSRs (PBALC 13, PBALC 206, and GLLC 563) associated with grain Fe concentration explaining 9% to 11% of phenotypic variation and four SSRs (PBALC 353, SSR 317-1, PLC 62, and PBALC 217) were associated with grain Zn concentration explaining 14%, to 21% of phenotypic variation. These identified SSRs exhibited consistent performance across locations. These candidate SSRs can be used in marker-assisted genetic improvement for developing Fe and Zn fortified lentil varieties. Favorable alleles and promising genotypes identified in this study can be utilized for lentil biofortification.

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.