Marker-trait Association Analysis Research Articles

Scanning the rice Global MAGIC population for dynamic genetic control of seed traits under vegetative drought

AbstractGrain size and shape are important yield components in rice (Oryza sativa L.), and their genetic control under adverse environmental conditions, such as drought stress, remains uncertain. This lack of knowledge is due to the laborious, time‐consuming phenotyping of seed attributes in large rice populations. We developed a new high‐throughput phenotyping method based on a desktop scanner and the open‐source package Plant Computer Vision (PlantCV). We used this method to investigate seed size and shape variability within the rice Global multi‐parent advanced generation intercross population, grown under well‐watered and vegetative drought conditions. Besides being affordable, rapid, and accurate, our method captured the phenotypic divergence between drought and well‐watered samples, expressed as 12 different traits, including new grain shape metrics. Our method facilitates the identification of outperforming genotypes under drought stress so is potentially very valuable for crop breeders seeking to make selection based on kernel attributes. We ran a marker–trait association analysis for the measured seed traits, demonstrating that our method also provides adequate phenotypes for genetic studies. We observed dynamic genetic control of seed‐related traits under vegetative drought stress, highlighting the importance of understanding the contribution of genotype × environment interactions on trait variation to develop resilient, high‐yielding rice cultivars.

Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.

Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

BackgroundImprovement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This study assessed quantitative trait nucleotides (QTNs) and the underlying candidate genes related to tuber yield per plant (TYP) and yam mosaic virus (YMV) tolerance in a panel of 406 white Guinea yam (Dioscorea rotundata) breeding lines using a genome-wide association study (GWAS).ResultsPopulation structure analysis using 5,581 SNPs differentiated the 406 genotypes into seven distinct sub-groups based delta K. Marker-trait association (MTA) analysis using the multi-locus linear model (mrMLM) identified seventeen QTN regions significant for TYP and five for YMV with various effects. The seveteen QTNs were detected on nine chromosomes, while the five QTNs were identified on five chromosomes. We identified variants responsible for predicting higher yield and low virus severity scores in the breeding panel through the marker-effect prediction. Gene annotation for the significant SNP loci identified several essential putative genes associated with the growth and development of tuber yield and those that code for tolerance to mosaic virus.ConclusionApplication of different multi-locus models of GWAS identified 22 QTNs. Our results provide valuable insight for marker validation and deployment for tuber yield and mosaic virus tolerance in white yam breeding. The information on SNP variants and genes from the present study would fast-track the application of genomics-informed selection decisions in breeding white Guinea yam for rapid introgression of the targeted traits through markers validation.

Genetic structure and molecular markers-trait association for physiological traits related to seed vigour in rice

Good quality seed is an important factor for a good crop and harvest. Vigour is the key performing trait of quality seed. Many physiological traits influence seed vigour in rice. Association of molecular markers with eleven physiological traits were investigated in a representative population. A representative population was constituted by including genotypes from all the phenotypic groups of the 11 physiological traits from the shortlisted population of 120 genotypes. The genotypic accessions with rich in multiple physiological traits were identified from the representative population. STRUCTURE, GenAlEx and Darwin software were used to classify the population. Generalized Linear Model (GLM) and Mixed Linear Models (MLM) were used in the marker-trait association analysis using the TASSEL software. Wide variations among the genotypic accessions were observed for the physiological traits estimated from the panel population. Linkage disequilibrium was detected for the 11 physiological traits in the panel population. STRUCTURE software classified the population into two genetic structure groups. Higher values of gene diversity and polymorphic information content (PIC) were estimated from the population based on genotyping using 50 simple sequence repeat markers. Genotypes present within groups and sub-groups showed similarity for their physiological traits. Strong association of the markers with physiological parameters namely RM167 for seed vigour index-I; RM7364 and RM235 for seed vigour index-II; RM440, RM223 for seedling dry weight; RM 256,RM25181, RM6547, RM328, RM201 for rate of root growth; RM 20, RM13335, RM216 for rate of shoot growth while RM20A and RM201 for absolute growth rate were detected by both GLM and MLM analyses. Markers detected in this association analysis may be potential use for future seed vigour improvement in rice.

Genome-Wide Association Mapping for Stomata and Yield Indices in Bread Wheat under Water Limited Conditions

Genome-wide association study (GWAS) was performed for stomata- and yield-related attributes with high-density Illumina 90 K Infinium SNP (single nucleotide polymorphism) array in bread wheat to determine genetic potential of germplasm for scarce water resources with sustainable yield potential. Major yield and stomata attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water shortage environments during two seasons. Highly significant variations were shown among accessions in both conditions for examined characteristics. Water shortage conditions reduced the overall wheat yield and strong positive correlation existed among stomatal frequency, leaf venation and grain yield per plant. Population structure analyses based on 90,000 SNP data classified the accessions into four sub-populations which indicated the presence of genetic variability. Marker-trait association (MTA) analyses revealed that 422 significant SNPs at p ≤ 10−3, after crossing the false discovery rate (FDR) <0.05 threshold, were linked with examined attributes. Pleiotropic loci (wsnp_Ex_c8913_14881924 and Tdurum_contig10598_304) were associated with flag leaf area (FLA), stomata size (SS), stomata frequency (SF), leaf venation (LV), number of grain per spike (NGS) and grain yield per plant (GYP), which were located on chromosome 4B and 6B at the positions 173.63cM and 229.64cM, respectively, under water shortage conditions. Pleotropic loci wsnp_Ex_c24167_33416760, wsnp_Ex_c5412_9564046 and Tdurum_contig81797_369 on chromosomes 7A, 2A and 4B at the positions 148.26cM, 261.05cM and 173.63cM, respectively, were significantly linked with stomata and yield indices such as FLA, SS, SF, LV, NGS and GYP under normal and water shortage conditions. The current experiment not only validated several MTAs for studied indices reported in other studies but also discovered novel MTAs significant under water shortage environments. Associated and significant SNPs will be useful in discovering novel genes underpinning water shortage tolerance in bread wheat for producing high-yielding and drought tolerant wheat varieties to fulfill the wheat demand for growing populations.

Development of EST-SSR markers and association analysis of floral scent in tree peony

Tree peony (Paeonia Sect. Moutan) is widely grown as an ornamental plant and is known for its ‘National Beauty and Heavenly Fragrance’. However, the genetic improvement of floral scent traits is fundamentally limited by the paucity of genomic marker resources. Given the large-scale development of microsatellite markers using transcriptome sequences, we conducted an association analysis to identify microsatellite markers associated with main floral components. A total of 8,443 EST-SSRs were identified, with an average of one SSR per 15.55 kb. Di-nucleotide repeats were the most plentiful repeat type, followed by tri-, tetra-, penta- and hexa-nucleotide repeats. Among 969 synthesized primer pairs, 499 were successfully amplified and 136 showed polymorphism which exhibited relatively high levels of transferability were observed across 12 individuals in the genus Paeonia, thus expanding their utility. Subsequently, 31 polymorphic EST-SSR markers were selected for the analysis of genetic diversity and population structure, resulting in 176 alleles; the polymorphism information content (PIC) varied from 0.31 to 0.87. According to the population structure analysis, the association varieties were divided into three subgroups. Finally, single marker-trait association analysis based on mixed linear model (MLM) identified 29 significant associations, involving five floral components with 18 SSRs and a low proportion of phenotypic variance ranging from 4.57 to 23.46%. The newly developed markers were valuable resources that could provide a powerful genomic tool for genetic studies and accelerate the process of molecular marker-assisted breeding of tree peony floral scent.

Genome-wide association mapping reveals key genomic regions for physiological and yield-related traits under salinity stress in wheat (Triticum aestivum L.)

A genome-wide association study (GWAS) was conducted using six different multi-locus GWAS models and 35K SNP array to demarcate genomic regions underlying reproductive stage salinity tolerance. Marker-trait association analysis was performed for salt tolerance indices (STI) of 11 morpho-physiological traits, and the actual concentrations of Na+ and K+, and the Na+/K+ ratio in flag leaf. A total of 293 significantly associated quantitative trait nucleotides (QTNs) for 14 morpho-physiological traits were identified. Of these 293 QTNs, 12 major QTNs with R2 ≥ 10.0% were detected in three or more GWAS models. Novel major QTNs were identified for plant height, number of effective tillers, biomass, grain yield, thousand grain weight, Na+ and K+ content, and the Na+/K+ ratio in flag leaf. Moreover, 48 candidate genes were identified from the associated genomic regions. The QTNs identified in this study could potentially be targeted for improving salinity tolerance in wheat.

Biotechnological Approaches for Genetic Improvement of Lemon (Citrus limon (L.) Burm. f.) against Mal Secco Disease.

Among Citrus species, lemon is one of the most susceptible to mal secco disease, a tracheomycosis caused by the mitosporic fungus Plenodomus tracheiphilus, which induces chlorosis followed by leaf drop and progressive desiccation of twigs and branches. Severe infection can cause the death of the plant. Since no effective control strategies are available to efficiently control the pathogen spread, host tolerance is the most desirable goal in the struggle against mal secco disease. To date, both traditional breeding programs and biotechnological techniques were not efficient in developing novel varieties coupling tolerance to mal secco with optimal fruit quality. Furthermore, the genetic basis of host resistance has not been fully deciphered yet, hampering the set-up of marker-assisted selection (MAS) schemes. This paper provides an overview of the biotechnological approaches adopted so far for the selection of mal secco tolerant lemon varieties and emphasizes the promising contribution of marker-trait association analysis techniques for both unraveling the genetic determinism of the resistance to mal secco and detecting molecular markers that can be readily used for MAS. Such an approach has already proved its efficiency in several crops and could represent a valuable tool to select novel lemon varieties coupling superior fruit quality traits and resistance to mal secco.

Association mapping of genomic loci linked with Fusarium wilt resistance (Foc2) in chickpea

AbstractImproving plant resistance against Fusarium wilt (FW) is key to sustaining chickpea production worldwide. Given this, the current study tested a set of 75 FW-responsive chickpea breeding lines including checks in a wilt-sick plot for two consecutive years (2016 and 2017). Genetic diversity analysis using 75 simple sequence repeats (SSRs) revealed a total of 267 alleles with an average of 3.56 alleles per marker. The entire set was divided into two major classes based on clustering method and factorial analysis. Similarly, STRUCTURE analysis placed the 75 genotypes into three distinct sub-groups (K = 3). Marker-trait association (MTA) analysis using the generalized linear model approach revealed nine and eight significant MTAs for FW resistance in the years 2016 and 2017, respectively. Three significant MTAs were obtained for FW resistance following the mixed linear model approach for both years. The SSR markers CESSR433, NCPGR21 and ICCM0284 could be potentially employed for targeted and accelerated improvement of FW resistance in chickpea. To the best of our knowledge, this is the first report on association mapping of the genomic loci controlling FW (Foc2) resistance in chickpea.

Marker-trait association analysis for drought tolerance in smooth bromegrass

BackgroundLittle 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.ResultsThe 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.ConclusionFollowing 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.

Effects of high temperature on spikelet sterility in rice (Oryza sativa L.): association between molecular markers and allelic phenotypic effect in field condition

Rice varieties are generally bred for higher yield but may possess genomic regions conferring tolerance to abiotic stresses. Climate change driven heat stress during reproductive stage of the crop affects spikelet fertility and yield. Though genetic regions associated with heat stress tolerance have been identified in rice, but response of rice varieties and allelic phenotypic effect favoring spikelet fertility during heat stress has not been comprehensively studied. Hence, the present study aimed at assessing the response of 198 rice varieties during the dry season (2016) followed by validation of selected 67 varieties in the second dry season (2017) through staggered sowing for high temperature. The analysis showed mean spikelet sterility of 21.82% and 33.81% for the first and second sowing, respectively. Further, average difference in spikelet sterility for unit increase in maximum temperature during the flowering period was observed to be 7.93%. Employment of nine heat stress associated markers for genetic analysis identified four sub-populations in the 67 varieties inferred through neighbor-joining phylogenetic tree and sub-structure analysis. Marker-trait association analysis showed two markers namely RM205, RM242 were significantly associated with spikelet sterility with phenotypic variance (R2) of 7.7% and 6.0%, respectively. Allelic phenotypic effect of favorable alleles for both the markers reduced spikelet sterility by 14.49% compared to mean spikelet sterility (33.81%). Furthermore, four rice varieties showed spikelet sterility < 15%. Thus, predominantly moderate tolerance to susceptible response was observed for rice varieties in this study. Besides, favorable allele of RM205, RM242 could be effectively used for improving tolerance in rice varieties to heat stress.

Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers.

Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts ofsequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.

Natural Variation and Domestication Selection of ZmCKX5 with Root Morphological Traits at the Seedling Stage in Maize.

Root system architecture plays a crucial role in water and nutrient acquisition in maize. Cytokinins, which can be irreversibly degraded by the cytokinin oxidase/dehydrogenase (CKX), are important hormones that regulate root development in plants. In this study, ZmCKX5 was resequenced in 285 inbred lines, 68 landraces, and 32 teosintes to identify the significant variants associated with root traits in maize. Sequence polymorphisms and nucleotide diversity revealed that ZmCKX5 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 12 variants of ZmCKX5 that were significantly associated with six root traits, including seed root number (SRN), lateral root length (LRL), total root area (RA), root length in 0 to 0.5 mm diameter class (RL005), total root volume (RV), and total root length (TRL). SNP-1195 explained the most (6.01%) phenotypic variation of SRN, and the frequency of this allele G increased from 6.25% and 1.47% in teosintes and landraces, respectively, to 17.39% in inbred lines. Another significant variant, SNP-1406, with a pleiotropic effect, is strongly associated with five root traits, with the frequency of T allele increased from 25.00% and 23.73% in teosintes and landraces, respectively, to 35.00% in inbred lines. These results indicate that ZmCKX5 may be involved in the development of the maize root system and that the significant variants can be used to develop functional markers to accelerate the improvement in the maize root system.

Association of polymorphisms of vasoactive intestinal peptide and its receptor with reproductive traits of turkey hens

The aim of this study was to identify variations of vasoactive intestinal peptide (VIP) and VIP receptor-1 (VIPR-1) genes that might be associated with turkey reproductive traits. One hundred twenty turkey hens were recorded for age at first egg (AFE), first egg weight (FEW), egg number (EN), total egg weight (TEW), laying period (LP), and broodiness. The DNA was isolated from blood samples and subjected to PCR amplification of the meleagrine VIP and VIPR-1 genes. The SNPs were detected by single-strand conformation polymorphism and the variant DNA fragments were sequenced. One mutation in 3’-UTR of VIP (G5846A) and two SNPs in intron 2 of VIPR-1 (C17687T and A17690T) were found, all of them novel. The associations of the three detected SNPs with the reproductive traits of turkeys were evaluated. The detected polymorphisms were used for marker-trait association analyses. The results of association analysis showed that G5846A on 3’ UTR of VIP has a significant association with LP, EN, TEW, and AFE. The G allele of G5846A was the favourable SNP allele for LP, EN, and TEW traits. The AA genotype of A17690T on intron 2 of VIPR-1 was significantly associated with higher LP, EN, and TEW. AGAA haplotype showed association with higher EN and TEW. These results suggest that the SNPs in 3’-UTR of VIP and intron 2 of VIPR-1 genes may influence egg production traits in turkey hens.Keywords: broodiness, candidate gene, egg production, single nucleotide polymorphism, VIPR-1

Genome-Wide Association Analysis for Tuber Dry Matter and Oxidative Browning in Water Yam (Dioscorea alata L.).

Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam.

Large-scale identification and characterization of phenolic compounds and their marker–trait association in wheat

Phenolic compounds (PCs) are important biomolecules as they affect processing (color, aroma, and taste quality of bread, and grain hardness) and nutrition quality (antioxidant and other health benefits). This study identified a set of 115 PCs by screening 100 Indian bread wheat varieties that showed wide variation in PCs content. These PCs were classified into 29 phenolic acid and their derivative, 71 flavonoids, 2 chalcones, 8 stilbenoids 1 theaflavin, 1 eugenol, and 3 coumarins. Of the 115, standards for 25 PCs were validated by matching their RT (retention time), MS and MS/MS fragmentation pattern on UPLC-QTOF-MS/MS. The range of PC content was from 0.01 µg/100 g for luteolin in ‘GW 503’ to 547.63 µg/100 g for vanillin in ‘Durgapur 65.’ The marker–trait association analysis identified 81 SSR markers which were associated with twelve PCs. Of 81, 53 were significantly associated on 5% FDR at true value (p < q). After multiple test correction (adjusted p value and 5% FDR), eight SSR markers were significantly associated with five PCs, namely ‘rutin,’ ‘hesperidin,’ ‘2,4-dihydroxybenzoic acid,’ ‘vanillin,’ and ‘salicylic acid.’ A substantial number of markers showed coefficient of variation (R2) ranged from ~ 5 to 45% for these PCs. The variations present in the set of wheat varieties and linked markers can be exploited for the improvement of PCs affecting processing and nutrition quality of wheat through molecular breeding and functional genomics tools.

Marker-Trait Association Analysis of Seed Traits in Accessions of Common Bean (Phaseolus vulgaris L.) in China.

Seed weight and seed size are the key agronomic traits that determine yield in common bean. To investigate the genetic architecture of four seed traits (100-seed weight, seed length, seed width, and seed height) of common bean in China, marker-trait association analysis of these seed traits was performed in a nationwide population of 395 common bean accessions using 116 polymorphic SSR markers. The four seed traits were evaluated in six trials across three environments. Seed size varied among the environments. Population structure was evaluated based on SSR markers and phaseolin, which divided the accessions into two main subpopulations representing the two known gene pools. Seed weight and seed size had a strong relationship with population clustering. In addition, in a Genome-wide association studies (GWAS), 21 significantly associated markers were identified for the four seed traits with two models, namely, general linear model (GLM) and mixed linear model (MLM). Some markers had pleiotropic effects, i.e., controlled more than one trait. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield in common bean.

Transmission Genetics of a Sorghum bicolor × S. halepense Backcross Populations.

Despite a “ploidy barrier,” interspecific crosses to wild and/or cultivated sorghum (Sorghum bicolor, 2n = 2x = 20) may have aided the spread across six continents of Sorghum halepense, also exemplifying risks of “transgene escape” from crops that could make weeds more difficult to control. Genetic maps of two BC1F1 populations derived from crosses of S. bicolor (sorghum) and S. halepense with totals of 722 and 795 single nucleotide polymorphism (SNP) markers span 37 and 35 linkage groups, with 2–6 for each of the 10 basic sorghum chromosomes due to fragments covering different chromosomal portions or independent segregation from different S. halepense homologs. Segregation distortion favored S. halepense alleles on chromosomes 2 (1.06–4.68 Mb, near a fertility restoration gene), 7 (1.20–6.16 Mb), 8 (1.81–5.33 Mb, associated with gene conversion), and 9 (47.5–50.1 Mb); and S. bicolor alleles on chromosome 6 (0–40 Mb), which contains both a large heterochromatin block and the Ma1 gene. Regions of the S. halepense genome that are recalcitrant to gene flow from sorghum might be exploited as part a multi-component system to reduce the likelihood of spread of transgenes or other modified genes. Its SNP profile suggests that chromosome segments from its respective progenitors S. bicolor and Sorghum propinquum have extensively recombined in S. halepense. This study reveals genomic regions that might discourage crop-to-weed gene escape, and provides a foundation for marker-trait association analysis to determine the genetic control of traits contributing to weediness, invasiveness, and perenniality of S. halepense.

Genetic Dissection of Phomopsis Stem Canker Resistance in Cultivated Sunflower Using High Density SNP Linkage Map.

Phomopsis stem canker (PSC) caused by Diaporthe helianthi is increasingly becoming a global threat for sunflower production. In this study, the genetic basis of PSC resistance was investigated in a recombinant inbred line (RIL) population developed from a cross between HA 89 (susceptible) and HA-R3 (resistant). The RIL population was evaluated for PSC disease incidence (DI) in seven screening trials at multiple locations during 2016–2018. The distribution of PSC DI in the RIL population was continuous, confirming a polygenic inheritance of the trait. A moderately high broad-sense heritability (H2, 0.76) was estimated for the trait across environments. In the combined analysis, both the genotype and the genotype × environment interactions were highly significant. A linkage map spanning 1505.33 cM was constructed using genotyping-by-sequencing derived markers. Marker–trait association analysis identified a total of 15 quantitative trait loci (QTL) associated with PSC resistance on 11 sunflower chromosomes, each explaining between 5.24 and 17.39% of the phenotypic variation. PSC resistance QTL were detected in two genomic regions each on chromosomes 3, 5, 13, and 17, while one QTL each was detected in the remaining seven chromosomes. Tightly linked single nucleotide polymorphism (SNP) markers flanking the PSC resistance QTL will facilitate marker-assisted selection in PSC resistance sunflower breeding.

Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection

In order to integrate genomics in breeding and development of drought-tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used 3249 diversity array technology sequencing (DArTSeq) markers for a genetic analysis of 125 ICRISAT groundnut mini core collection evaluated in 2015 and 2017 for genome-wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD). Marker-trait association (MTA) analysis, probability values, and percent variation modelled by the markers were calculated using the GAPIT package via the KDCompute interface. The LD analysis showed that about 36% of loci pairs were in significant LD (p &lt; 0.05 and r2 &gt; 0.2) and 3.14% of the pairs were in complete LD. The MTAs studies revealed 20 significant MTAs (p &lt; 0.001) with 11 markers. Four MTAs were identified for leaf area index, 13 for canopy temperature, one for chlorophyll content and two for normalized difference vegetation index. The markers explained 20.8% to 6.6% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. This could be due to a common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance after further validation.