Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions

Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF)?≥?0.05 were detected across the 20 chromosomes (Chr), with a marker density of 78.7 kbp. A total of 31 SNPs located on 12 of the 20 soybean chromosomes were correlated with seed protein and oil content. Of the 31 SNPs that were associated with the two target traits, 31 beneficial alleles were identified. Two SNP markers, namely rs15774585 and rs15783346 on Chr 07, were determined to be related to seed oil content both in 2015 and 2016. Three SNP markers, rs53140888 on Chr 01, rs19485676 on Chr 13, and rs24787338 on Chr 20 were correlated with seed protein content both in 2015 and 2016. These beneficial alleles may potentially contribute towards the MAS of favorable soybean protein and oil characteristics.     

Association analysis of salt tolerance in cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp) at germination and seedling stages

Key message

This is the first report on association analysis of salt tolerance and identification of SNP markers associated with salt tolerance in cowpea.

Abstract

Cowpea (Vigna unguiculata (L.) Walp) is one of the most important cultivated legumes in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetic underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt-tolerant cowpea cultivars. The objectives of this study were to conduct association mapping for salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. We analyzed the salt tolerance index of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1049 SNPs postulated from genotyping-by-sequencing were used for association analysis. Population structure was inferred using Structure 2.3.4; K optimal was determined using Structure Harvester. TASSEL 5, GAPIT, and FarmCPU involving three models such as single marker regression, general linear model, and mixed linear model were used for the association study. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were structured into two subpopulations. Three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage. Seven SNPs, Scaffold93827_270, Scaffold68489_600, Scaffold87490_633, Scaffold87490_640, Scaffold82042_3387, C35069468_1916, and Scaffold93942_1089 were found to be associated with salt tolerance at seedling stage. The SNP markers were consistent across the three models and could be used as a tool to select salt-tolerant lines for breeding improved cowpea tolerance to salinity.

     

Mapping QTLs conferring salt tolerance during germination in tomato by selective genotyping

This study was conducted to identify genomic regions (quantitative trait loci, QTLs) affecting salt tolerance during germination in tomato. Germination response of an F2 population of a cross between UCT5 (Lycopersicon esculentum, salt-sensitive) and LA716 (L. pennellii, salt-tolerant) was evaluated at a salt-stress level of 175 mM NaCl + 17.5 mM CaCl2 (water potential ca. –950 kPa). Germination was scored visually as radicle protrusion at 6 h intervals for 30 consecutive days. Individuals at both extremes of the response distribution (i.e., salt-tolerant and salt-sensitive individuals) were selected. The selected individuals were genotyped at 84 genetic markers including 16 isozymes and 68 restriction fragment length polymorphisms (RFLPs). Trait-based marker analysis (TBA) which measures changes (differences) in marker allele frequencies in selected lines was used to identify marker-linked QTLs. Eight genomic regions were identified on seven tomato chromosomes bearing genes (QTLs) with significant effects on this trait. The results confirmed our previous suggestion that salt tolerance during germination in tomato is polygenically controlled. The salt-tolerant parent contributed favorable QTL alleles on chromosomes 1, 3, 9 and 12 whereas the salt sensitive parent contributed favorable QTL alleles on chromosomes 2, 7 and 8. The identification of favorable alleles in both parents suggests the likelihood of recovering transgressive segregants in progeny derived from these parental genotypes. The results can be used for marker-assisted selection and breeding of salt-tolerant tomatoes.     

Mapping and confirmation of loci for salt tolerance in a novel soybean germplasm,Fiskeby III

Key message

The confirmation of a major locus associated with salt tolerance and mapping of a new locus, which could be beneficial for improving salt tolerance in soybean.

Abstract

Breeding soybean for tolerance to high salt conditions is important in some regions of the USA and world. Soybean cultivar Fiskeby III (PI 438471) in maturity group 000 has been reported to be highly tolerant to multiple abiotic stress conditions, including salinity. In this study, a mapping population of 132 F₂ families derived from a cross of cultivar Williams 82 (PI 518671, moderately salt sensitive) and Fiskeby III (salt tolerant) was analyzed to map salt tolerance genes. The evaluation for salt tolerance was performed by analyzing leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC) after treatment with 120 mM NaCl under greenhouse conditions. Genotypic data for the F₂ population were obtained using the SoySNP6K Illumina Infinium BeadChip assay. A major allele from Fiskeby III was significantly associated with LSS, CCR, LSC, and LCC on chromosome (Chr.) 03 with LOD scores of 19.1, 11.0, 7.7 and 25.6, respectively. In addition, a second locus associated with salt tolerance for LSC was detected and mapped on Chr. 13 with an LOD score of 4.6 and an R ² of 0.115. Three gene-based polymorphic molecular markers (Salt-20, Salt14056 and Salt11655) on Chr.03 showed a strong predictive association with phenotypic salt tolerance in the present mapping population. These molecular markers will be useful for marker-assisted selection to improve salt tolerance in soybean.

     

Identification and validation of QTLs for salt tolerance during vegetative growth in tomato by selective genotyping.

The purpose of this study was to identify quantitative trait loci (QTLs) for salt tolerance (ST) during vegetative growth (VG) in tomato by distributional extreme analysis and compare them with the QTLs previously identified for this trait. A BC1 population (N = 792) of a cross between a moderately salt-sensitive Lycopersicon esculentum Mill. breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant L. pimpinellifolium (Jusl.) Mill. accession (LA722) was evaluated for ST in solution cultures containing 700 mM NaCl + 70 mM CaCl2 (electrical conductivity, EC = 64 dS/m and phiw approximately -35.2 bars). Thirty-seven BC1 plants (4.7% of the total) that exhibited the highest ST were selected (referred to as the selected population), grown to maturity in greenhouse pots and self-pollinated to produce BC1S1 progeny seeds. The 37 selected BC1S1 progeny families were evaluated for ST and their average performance was compared with that of the parental BC1 population before selection. A realized heritability of 0.50 was obtained for ST in this population. The 37 selected BC1 plants were subjected to restriction fragment length polymorphism (RFLP) analysis using 115 markers, and marker allele frequencies were determined. Allele frequencies for the same markers were also determined in an unselected BC1 population (N = 119) of the same cross. A trait-based marker analysis (TBA), which measures differences in marker allele frequencies between selected and unselected populations, was used to identify marker-linked QTLs. Five genomic regions were detected on chromosomes 1, 3, 5, 6, and 11 bearing significant QTLs for ST. Except for the QTL on chromosome 3, all QTLs had positive alleles contributed from the salt tolerant parent LA722. Of the five QTLs, three (those on chromosomes 1, 3, and 5) were previously identified for this trait in another study, and thus were validated here. Only one of the major QTLs that was identified in our previous study was not detected here. This high level of conformity between the results of the two studies indicates the genuine nature of the identified QTLs and their potential usefulness for ST breeding using marker-assisted selection (MAS). A few BC1S1 families were identified with most or all of the QTLs and with a ST comparable to that of LA722. These families should be useful for the development of salt tolerant tomato lines via MAS.     

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

The key to plant survival under NaCl salt stress is maintaining a low Na⁺ level or Na⁺/K⁺ ratio in the cells. A population of recombinant inbred lines (RILs, F_2∶9) derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na⁺ and K⁺ concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na⁺ in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na⁺ in shoots (SNC), four additive QTLs identified for K⁺ in roots (RKC), four additive QTLs and three epistatic QTLs identified for K⁺ in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.     

Identification of QTLs with main, epistatic and QTL?×?environment interaction effects for salt tolerance in rice seedlings under different salinity conditions

Salt tolerance of rice (Oryza sativa L.) at the seedling stage is one of the major determinants of its stable establishment in saline soil. One population of recombinant inbred lines (RILs, F (2:9)) derived from a cross between the salt-tolerant variety Jiucaiqing and the salt-sensitive variety IR26 was used to determine the genetic mechanism of four salt tolerance indices, seedling height (SH), dry shoot weight (DSW), dry root weight (DRW) and Na/K ratios (Na/K) in roots after 10 days in three salt concentrations (0.0, 0.5 and 0.7 % NaCl). The main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) were detected by QTL IciMapping program using single environment phenotypic values. Eleven M-QTLs and 11 E-QTLs were identified for the salt tolerance indices. There were six M-QTLs and two E-QTLs identified for SH, three M-QTLs and five E-QTLs identified for DSW, two M-QTLs and one E-QTL identified for DRW, and three E-QTLs identified for Na/K. The phenotypic variation explained by each M-QTL and E-QTL ranged from 7.8 to 23.9 % and 13.3 to 73.7 %, respectively. The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values. Six M-QTLs and five E-QTLs were identified. The phenotypic variation explained by each QTL and QTL × environment interaction ranged from 0.95 to 6.90 % and 0.02 to 0.50 %, respectively. By comparing chromosomal positions of these M-QTLs with those previously identified, five M-QTLs qSH1.3, qSH12.1, qSH12.2, qDSW12.1 and qDRW11 might represent novel salt tolerance genes. Five selected RILs with high salt tolerance had six to eight positive alleles of the M-QTLs, indicating that pyramiding by marker-assisted selection (MAS) of M-QTLs can be applied in rice salt tolerance breeding programs.     

Recent Advances in Genetics of Salt Tolerance in Tomato

Salinity is an important environmental constraint to crop productivity in arid and semi-arid regions of the world. Most crop plants, including tomato, Lycopersicon esculentum Mill., are sensitive to salinity throughout the ontogeny of the plant. Despite considerable research on salinity in plants, there are only a few instances where salt-tolerant cultivars have been developed. This is due in part to the complexity of the trait. A plant's response to salt stress is modulated by many physiological and agronomical characteristics, which may be controlled by the actions of several to many genes whose expressions are influenced by various environmental factors. In addition, salinity tolerance is a developmentally regulated, stage-specific phenomenon; tolerance at one stage of plant development is often not correlated with tolerance at other stages. Specific ontogenic stages should be evaluated separately for the assessment of tolerance and the identification, characterization, and utilization of useful genetic components. In tomato, genetic resources for salt tolerance have been identified largely within the related wild species, and considerable efforts have been made to characterize the genetic controls of tolerance at various developmental stages. For example, the inheritance of several tolerance-related traits has been determined and quantitative trait loci (QTLs) associated with tolerance at individual developmental stages have been identified and characterized. It has been determined that at each stage salt tolerance is largely controlled by a few QTLs with major effects and several QTLs with smaller effects. Different QTLs have been identified at different developmental stages, suggesting the absence of genetic relationships among stages in tolerance to salinity. Furthermore, it has been determined that in addition to QTLs which are population specific, several QTLs for salt tolerance are conserved across populations and species. Research is currently underway to develop tomatoes with improved salt tolerance throughout the ontogeny of the plant by pyramiding QTLs through marker-assisted selection (MAS). Transgenic approaches also have been employed to gain a better understanding of the genetics of salt tolerance and to develop tomatoes with improved tolerance. For example, transgenic tomatoes with overexpression of a single-gene-controlled vacuolar Na⁺/H⁺ antiport protein, transferred from Arabidopsis thaliana, have exhibited a high level of salt tolerance under greenhouse conditions. Although transgenic plants are yet to be examined for field salt tolerance and salt-tolerant tomatoes are yet to be developed by MAS, the recent genetic advances suggest a good prospect for developing commercial cultivars of tomato with enhanced salt tolerance in near future.     

大豆耐盐机理及相关基因分子标记

大豆耐盐涉及多种生理代谢途径。耐盐大豆能够通过Cl-排除、控制Na+的吸收和转运、合成渗透调节物质、改变细胞膜膜脂组分及相关酶类的活性等多种形式来适应盐胁迫;野生大豆群体具有盐腺,从形态结构上适应盐逆境;大豆-根瘤菌共生体在盐胁迫下通过互作来提高整体的耐盐性。分子生物学技术应用于大豆耐盐研究,已获得了一些与耐盐相关基因连锁的分子标记。广泛搜集筛选大豆栽培种和野生种资源,利用分子生物学技术和基因工程提高大豆耐盐性,将成为未来大豆耐盐研究的主要内容。     

盐胁迫对海岛棉和陆地棉幼苗生长及生理特性的影响

采用盆栽法,以海岛棉(Gossypium barbadense)品种新海21号、新海34号和陆地棉(G.hirsutum)品种新陆早50号、新陆早57号为材料,探讨了盐胁迫下海岛棉和陆地棉植株的生长、叶绿素含量、净光合速率、蒸腾速率、抗氧化酶活性、渗透调节物质及丙二醛含量变化的差异。结果显示,随着盐浓度的增加,4个供试品种幼苗的生长、叶绿素含量、净光合速率、蒸腾速率均呈不同程度的下降,而过氧化物酶、超氧化物歧化酶及可溶性糖含量随着盐浓度的增加呈先增后降的趋势,脯氨酸和丙二醛含量均上升。不同品种之间,新海21号和新海34号受胁迫的影响程度小于新陆早57号和新陆早50号。在0.6%Na Cl胁迫下,海岛棉和陆地棉品种均表现出较好的耐盐性。而0.8%和1.0%的Na Cl胁迫对4个供试品种的生长抑制作用大,导致新陆早57号和新陆早50号幼苗生长缓慢、叶面积小、干物质积累少甚至死苗。在较高浓度的盐胁迫下,棉花品种幼苗第1片真叶展开受到显著抑制,可以作为棉花耐盐品种的筛选指标。     

Genetic analysis of physiological components of salt tolerance conferred by Solanum rootstocks. What is the rootstock doing for the scion?

Grafting desirable crop varieties on stress-tolerant rootstocks provides an opportunity to increase crop salt tolerance. Here, a commercial hybrid tomato variety was grafted on two populations of recombinant inbred lines developed from a salt-sensitive genotype of Solanum lycopersicum var. cerasiforme, as female parent, and two salt-tolerant lines, as male parents, from S. pimpinellifolium, the P population, and S. cheesmaniae, the C population, to identify an easy screening method for identifying rootstocks conferring salt tolerance in terms of fruit yield. Potential physiological components of salt tolerance were assessed in the scion: leaf biomass, [Na⁺], nutrition, water relations and xylem ABA concentration. A significant correlation between scion fruit yield and scion leaf fresh weight, water potential or the ABA concentration was found in the C population under salinity, but the only detected QTL did not support this relationship. The rootstocks of the P population clearly affected seven traits related to the sodium, phosphorous and copper concentrations and water content of the scion leaf, showing heritability estimates around 0.4 or higher. According to heritability estimates in the P population, up to five QTLs were detected per trait. QTLs contributing over 15% to the total variance were found for P and Cu concentrations and water content of the scion leaf, and the proportion of fresh root weight. Correlation and QTL analysis suggests that rootstock-mediated improvement of fruit yield in the P population under salinity is mainly explained by the rootstock’s ability to minimise perturbations in scion water status.     

Identification of a major QTL allele from wild soybean (Glycine soja Sieb. & Zucc.) for increasing alkaline salt tolerance in soybean

Salt-affected soils are generally classified into two main categories, sodic (alkaline) and saline. Our previous studies showed that the wild soybean accession JWS156-1 (Glycine soja) from the Kinki area of Japan was tolerant to NaCl salt, and the quantitative trait locus (QTL) for NaCl salt tolerance was located on soybean linkage group N (chromosome 3). Further investigation revealed that the wild soybean accession JWS156-1 also had a higher tolerance to alkaline salt stress. In the present study, an F₆ recombinant inbred line mapping population (n = 112) and an F₂ population (n = 149) derived from crosses between a cultivated soybean cultivar Jackson and JWS156-1 were used to identify QTL for alkaline salt tolerance in soybean. Evaluation of soybean alkaline salt tolerance was carried out based on salt tolerance rating (STR) and leaf chlorophyll content (SPAD value) after treatment with 180 mM NaHCO₃ for about 3 weeks under greenhouse conditions. In both populations, a significant QTL for alkaline salt tolerance was detected on the molecular linkage group D2 (chromosome 17), which accounted for 50.2 and 13.0% of the total variation for STR in the F₆ and the F₂ populations, respectively. The wild soybean contributed to the tolerance allele in the progenies. Our results suggest that QTL for alkaline salt tolerance is different from the QTL for NaCl salt tolerance found previously in this wild soybean genotype. The DNA markers closely associated with the QTLs might be useful for marker-assisted selection to pyramid tolerance genes in soybean for both alkaline and saline stresses.     

Unlocking Allelic Diversity for Sustainable Development of Salinity Stress Tolerance in Rice

Rice is a major cereal crop, negatively impacted by soil-salinity, both in terms of plant growth as well as productivity. Salinity tolerant rice varieties have been developed using conventional breeding approaches, however, there has been limited success which is primarily due to the complexity of the trait, low yield, variable salt stress response and availability of genetic resources. Furthermore, the narrow genetic base is a hindrance for further improvement of the rice varieties. Therefore, there is a greater need to screen available donor germplasm in rice for salinity tolerance related genes and traits. In this regard, genomics based techniques are useful for exploring new gene resources and QTLs. In rice, the vast allelic diversity existing in the wild and cultivated germplasm needs to be explored for improving salt tolerance. In the present review, we provide an overview of the allelic diversity in the Quantitative Trait Loci (QTLs) like Saltol, qGR6.2, qSE3 and RNC4 as well as genes like OsHKT1;1, SKC1 (OsHKT1;5/HKT8) and OsSTL1 (salt tolerance level 1 gene) related to salt tolerance in rice. We have also discussed approaches for developing salt-tolerant cultivars by utilizing the effective QTLs or genes/alleles in rice.     

Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.)

Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses.     

Quantitative trait loci (QTL) mapping for physiological and biochemical attributes in a Pasban90/Frontana recombinant inbred lines (RILs) population of wheat (Triticum aestivum) under salt stress condition

Salt stress causes nutritional imbalance and ion toxicity which affects wheat growth and production. A population of recombinant inbred lines (RILs) were developed by crossing Pasban90 (salt tolerant) and Frontana (salt suceptible) for identification of quantitative trait loci (QTLs) for physiological traits including relative water content, membrane stability index, water potential, osmotic potential, total chlorophyll content, chlorophyll a, chlorophyll b and biochemical traits including proline contents, superoxide dismutase, sodium content, potassium content, chloride content and sodium/potassium ratio by tagging 202 polymorphic simple sequence repeats (SSR) markers. Linkage map of RILs comprised of 21 linkage group covering A, B and D genome for tagging and maped a total of 60 QTLs with major and minor effect. B genome contributed to the highest number of QTLs under salt stress condition. Xgwm70 and Xbarc361 mapped on chromosome 6B was linked with Total chlorophyll, water potential and sodium content. The increasing allele for all these QTLs were advanced from parent Pasban90. Current study showed that Genome B and D had more potentially active genes conferring plant tolerance against salinity stress which may be exploited for marker assisted selection to breed salinity tolerant high yielding wheat varieties.     

In silico single nucleotide polymorphism discovery and application to marker-assisted selection in soybean

The general approach to discovering single nucleotide polymorphisms (SNPs) requires locus-specific PCR amplification. To enhance the efficiency of SNP discovery in soybean, we used in silico analysis prior to re-sequencing as it is both rapid and inexpensive. In silico analysis was performed to detect putative SNPs in expressed sequence tag (EST) contigs assembled using publicly available ESTs from 18 different soybean genotypes. SNP validation by direct sequencing of six soybean cultivars and a wild soybean genotype was performed with PCR primers designed from EST contigs aligned with at least 5 out of 18 soybean genotypes. The efficiency of SNP discovery among the confirmation genotypes was 81.2%. Furthermore, the efficiency of SNP discovery between Pureunkong and Jinpumkong 2 genotypes was 47.4%, a great improvement on our previous finding based on direct sequencing (22.3%). Using SNPs between Pureunkong and Jinpumkong 2 in EST contigs, which were linked to target traits, we were able to genotype 90 recombinant inbred lines by high-resolution melting (HRM) analysis. These SNPs were mapped onto the expected locations near quantitative trait loci for water-logging tolerance and seed pectin concentration. Thus, our protocol for HRM analysis can be applied successfully not only to genetic diversity studies, but also to marker-assisted selection (MAS). Our study suggests that a combination of in silico analysis and HRM can reduce the cost and labor involved in developing SNP markers and genotyping SNPs. The markers developed in this study can also easily be applied to MAS if the markers are associated with the target traits.     

Rapid genotyping of soybean cultivars using high throughput sequencing

Soybean (Glycine max) breeding involves improving commercially grown varieties by introgressing important agronomic traits from poor yielding accessions and/or wild relatives of soybean while minimizing the associated yield drag. Molecular markers associated with these traits are instrumental in increasing the efficiency of producing such crosses and Single Nucleotide Polymorphisms (SNPs) are particularly well suited for this task, owing to high density in the non-genic regions and thus increased likelihood of finding a tightly linked marker to a given trait. A rapid method to develop SNP markers that can differentiate specific loci between any two parents in soybean is thus highly desirable. In this study we investigate such a protocol for developing SNP markers between multiple soybean accessions and the reference Williams 82 genome. To restrict sampling frequency reduced representation libraries (RRLs) of genomic DNA were generated by restriction digestion followed by library construction. We chose to sequence four accessions Dowling (PI 548663), Dwight (PI 597386), Komata (PI200492) and PI 594538A for their agronomic importance as well as Williams 82 as a control.MseI was chosen to digest genomic DNA based on predictions that it will cut sparingly in the mathematically defined high-copy-number regions of the genome. All RRLs were sequenced on the Illumina genome analyzer. Reads were aligned to the Glyma1 reference assembly and SNP calls made from the alignments. We identified from 4294 to 14550 SNPs between the four accessions and the Williams 82 reference. In addition a small number of SNPs (1142) were found by aligning Williams 82 reads to the reference assembly (Glyma1) suggesting limited genetic variation within the Williams 82 line. The SNP data allowed us to estimate genetic diversity between the four lines and Williams 82. Restriction digestion of soybean genomic DNA with MseI followed by high throughput sequencing provides a rapid and reproducible method for generating SNP markers.     

Sugar accumulation,photosynthesis and growth of two indica rice varieties in response to salt stress

Sugar, a final product of photosynthesis, is reported to be involved in the defense mechanisms of plants against abiotic stresses such as salinity, water deficiency, extreme temperature and mineral toxicity. Elements involved in photosynthesis, sugar content, water oxidation, net photosynthetic rate, activity of enzyme and gene expression have therefore been studied in Homjan (HJ), salt-tolerant, and Pathumthani 1 (PT1), salt-sensitive, varieties of rice. Fructose-1,6-biphosphatase (FBP) and fructokinase (FK) genes were rapidly expressed in HJ rice when exposed to salt stress for 1–6 h and to a greater degree than in PT1 rice. An increase in FBP enzyme activity was found in both roots and leaves of the salt-tolerant variety after exposure to salt stress. A high level of sugar and a delay in chlorophyll degradation were found in salt-tolerant rice. The total sugar content in leaf and root tissues of salt-tolerant rice was 2.47 and 2.85 times higher, respectively, than in the salt-sensitive variety. Meanwhile, less chlorophyll degradation was detected. Salt stress may promote sugar accumulation, thus preventing the degradation of chlorophyll. Water oxidation by the light reaction of photosynthesis in the salt-tolerant variety was greater than that in the salt-sensitive variety, indicated by a high maximum quantum yield of PSII (F _v/F _m) and quantum efficiency of PSII (Φ_PSII) with low nonphotochemical quenching (NPQ), leading to a high net photosynthetic rate. In addition, the overall growth performances in the salt-tolerant variety were higher than those in the salt-sensitive variety. The FBP gene expression and enzyme activity, sugar accumulation, pigment stabilization, water oxidation and net photosynthetic rate parameters in HJ rice should be further investigated as multivariate salt-tolerant indices for the classification of salt tolerance in rice breeding programs.