Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions （Gossypium hirsutum L.）

Exploring the elite al eles and germplasm acces-sions related to fiber quality traits wil accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatel ite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite al eles associated simulta-neously with two or three traits. These elite al eles were mainly from accessions col ected in China, introduced to China from the United States, or rare al eles with a frequency of less than＆amp;nbsp;5%. No one cultivar contained more than half of the elite al eles, but 10 accessions were col ected from China and the two introduced from the United States did contain more than half of these al eles. Therefore, there is great potential for mining elite al eles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.     

棉花萌发期和苗期耐盐性评价及耐盐指标筛选

于2010年在江苏南京农业大学人工气候室内进行砂培试验,采用不同浓度的NaCl水溶液模拟盐胁迫,以多项指标盐害系数隶属函数值和总隶属函数值为依据,比较了13个棉花品种萌发期和苗期的耐盐性,并进行聚类分析.结果表明:150mmol·L-1NaCl是进行棉花耐盐性鉴定的适宜盐浓度.棉花的耐盐性在生育期和品种间表现不同:中棉所44和中棉所177是在萌发期和苗期均表现稳定的耐盐品种,表现稳定但不耐盐品种有中棉所102、苏棉12号和泗棉3号,表现稳定且中等耐盐品种有中棉所103、德夏棉1号和美棉33B;发芽率、发芽势、发芽指数、活力指数和鲜质量的盐害系数可以作为棉花萌发期耐盐鉴定指标,株高、叶片伸展速率、地上部干质量、根系干质量、根系活力和净光合速率的盐害系数可以作为棉花苗期耐盐鉴定指标.     

陆地棉萌发至三叶期不同生育阶段耐盐特性

摘要：土壤盐渍化是一个世界性的资源问题和生态问题,盐分胁迫几乎会影响棉花所有重要的生命活动, 造成棉花的减产或其他不利影响。本试验通过对14个品棉花种（系）的萌发期耐盐性、芽期耐盐性以及两个耐盐性不同的品种（系）三叶期的耐盐性,对棉花不同时期的耐盐特性进行了研究,结果表明：棉花在不同生育阶段耐盐能力是不同的,棉花盐敏感时间是在萌发出苗期。随着生育期的延长,棉花的耐盐性是逐步提高的,进行耐盐性鉴定的最佳时期在是萌发出苗期。在三叶期,随着盐分浓度的提高,棉花苗受伤害程度逐渐增加,盐敏感性品种受伤害大于耐盐品种,在同样盐浓度胁迫条件下,耐盐性不同的品种各部分受到的伤害不同,耐盐品种（系）中棉所35受伤害程度由高到低依次为：真叶>上胚轴>子叶;盐敏感品种（系）Tamcot CAB-CS受伤害程度由高到低依次为：真叶> 子叶>上胚轴。     

Detection of favorable alleles for yield and yield components by association mapping in upland cotton

Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(??lgP?>?1.30, P?<?0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci’s alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.     

部分耐盐小麦品种(系)SSR位点遗传多样性研究

选择有多态性的32对SSR引物对80个小麦耐盐品种(系)进行遗传差异研究,共检测出155个等位变异,平均每个位点上有4.75个等位变异;供试80份耐盐小麦品种(系)来源广泛,遗传基础丰富,表现出较高的遗传多样性,遗传相似系数范围在0.26～0.81;聚类分析结果显示,冬性小麦品种(系)聚为一大类;春性小麦品种(系)也聚为一大类;一些系谱相同或相近的品种(系)遗传相似系数较大;A、B、D基因组中SSR位点平均等位变异差异不大,以B基因组较高.     

Genetic architecture of NaCl tolerance in Arabidopsis

The little success of breeding approaches toward the improvement of salt tolerance in crop species is thought to be attributable to the quantitative nature of most, if not all the processes implicated. Hence, the identification of some of the quantitative trait loci (QTL) that contribute to natural variation in salt tolerance should be instrumental in eventually manipulating the perception of salinity and the corresponding responses. A good choice to reach this goal is the plant model system Arabidopsis, whose complete genome sequence is now available. Aiming to analyze natural variability in salt tolerance, we have compared the ability of 102 wild-type races (named ecotypes or accessions) of Arabidopsis to germinate on 250 mM NaCl, finding a wide range of variation among them. Accessions displaying extremely different responses to NaCl were intercrossed, and the phenotypes found in their F(2) progenies suggested that natural variation in NaCl tolerance during germination was under polygenic controls. Genetic distances calculated on the basis of variations in repeat number at 22 microsatellites, were analyzed in a group of either extremely salt-tolerant or extremely salt-sensitive accessions. We found that most but not all accessions with similar responses to NaCl are phylogenetically related. NaCl tolerance was also studied in 100 recombinant inbred lines derived from a cross between the Columbia-4 and Landsberg erecta accessions. We detected 11 QTL harboring naturally occurring alleles that contribute to natural variation in NaCl tolerance in Arabidopsis, six at the germination and five at the vegetative growth stages, respectively. At least five of these QTL are likely to represent loci not yet described by their relationship with salt stress.     

甜菜耐盐性筛选及其幼苗对盐胁迫的响应

为了探讨甜菜耐盐机理、不同耐盐等级甜菜盐耐性机制差异,对40份甜菜品种（系）用300mmol·L-1NaCl胁迫处理,通过芽期相对盐害率和苗期盐害指数确定不同品种耐盐等级,将不同耐盐等级材料进行NaCl浓度梯度（150、300mmol·L-1）处理,测定植株鲜重、超氧化物歧化酶（SOD）活性、丙二醛（MDA）含量和叶片质膜透性。试验结果如下：40份甜菜材料经过芽期和苗期耐盐性筛选最终确定耐盐等级极强的品种（系）1份（‘KWS0143’）,耐盐等级强的品种（系）6份（‘ACERO’等）,耐盐等级中等的品种（系）14份（‘HI0183’等）,耐盐等级弱的品种（系）5份（‘OVITO’等）;在同一盐胁迫时间下,不同耐盐等级材料的植株鲜重随盐浓度的增加呈下降趋势,品种‘KWS0143’和‘ACERO’变化幅度较小,品种‘OVATIO’下降幅度最大;不同耐盐等级材料随盐浓度增加和胁迫时间延长超氧化物歧化酶（SOD）活性呈现先上升而后下降的趋势,耐盐性极强的品种酶活性显著高于其他耐盐等级材料;不同耐盐等级材料随盐浓度增加和胁迫时间延长丙二醛（MDA）含量和叶片质膜透性均呈上升趋势,耐盐等级弱的品种（系）明显高于其他各个材料。     

From the editor’s desk

Improving cotton fibre quality is a major breeding goal for Upland cotton in China. To investigate the genetic mechanisms of fibre quality, a diverse panel of 403 Upland cotton accessions was grown, and the fibre quality traits were measured in six different environments. Genotyping was performed with genomewide simple sequence repeats. A total of 201 markers were polymorphic and generated 394 allele loci, and 403 accessions were arranged into two subgroups using Structure software. Of the marker loci, 18.94% showed significant linkage disequilibrium (\(P< 0.05\)). A mixed linear model in association mapping showed that 51 associations were significant between 39 polymorphic loci and five fibre quality traits, according to best linear unbiased prediction, and in at least three of six environments. Of the 39 associated marker loci, 12 were coincident with previous studies. There were 41 typical accessions identified as containing favourable allele loci related to fibre quality traits. The identified favourable QTL alleles and typical accessions for fibre quality are excellent genetic resources for future cotton breeding in China.     

Genetic variability of NaCl tolerance in tomato

Cultivation of crops in soils with high salt (NaCl) content can affect plant development. We examined the morphological and physiological mechanisms of salt tolerance in tomato. The responses of 72 accessions of tomato (Solanum lycopersicum) to salinity were compared by measuring shoot and root lengths, and fresh shoot and root weights relative to those of controls (plants grown in normal salt levels). All traits were reduced at the seedling stage when salinity levels were increased. The accession x salinity interaction was significant for all traits. Root length had higher heritability than other traits and was used as a selection criterion to identify salt-tolerant and -non-tolerant accessions. On the basis of root length, accessions LA2661, CLN2498A, CLN1621L, BL1176, 6233, and 17870 were considered to be more tolerant than accessions 17902, LO2875 and LO4360. The degree of salt tolerance was checked by analyzing K+ and Na+ concentrations and K+/Na+ ratio in tissues of plants treated with 10 and 15 dS/m salinity levels. Tolerance of these accessions to salinity was most associated with low accumulation of Na+ and higher K+/Na+ ratios.     

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na⁺/K⁺ ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na⁺/K⁺ ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.     

Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis

For broadening the narrow genetic base of modern soybean cultivars, 159 accessions were selected from the Chinese soybean collection which contained at least one of seven important agronomic traits: resistance to soybean cyst nematode (SCN) or soybean mosaic virus (SMV), tolerance to salt, cold, or drought, high seed oil content or high protein content. Genetic diversity evaluation using 55 microsatellite loci distributed across the genome indicated that a large amount of genetic diversity (0.806) and allelic variation (781) were conserved in this selected set, which captured 65.6% of the alleles present in Chinese soybean collection (1,863 accessions). On average, 9.4 rare alleles (frequency <5%) per locus were present, which were highly informative. Using model-based Bayesian clustering in STRUCTURE we distinguished four main clusters and a set of accessions with admixed ancestry. The four clusters reflected different geographic regions of origin of the accessions. Since the clusters were also clearly different with respect to the seven agronomic traits, the inferred population structure was introduced when association analysis was conducted. A total of 21 SSR markers on 16 chromosomes were identified as significantly (P < 0.01) associated with high oil content (6), high protein content (1), drought tolerance (5), SCN resistance (6) and SMV resistance (3). Twelve of these markers were located in or near previously identified quantitative trait loci (QTL). The results for both genetic relationship and trait-related markers will be useful for effective conservation and utilization of soybean germplasm.     

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.     

Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon

Soil salinity is one of the major abiotic stresses affecting plant growth and crop production.In the present study,salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ILs),which were derived from a cross between an elite indica cultivar Teqing and an accession of common wild rice (Oryza rufipogon Griff.).Substantial variation was observed for four traits including salt tolerance score (STS),relative root dry weight (RRW),relative shoot dry weight (RSW) and relative total dry weight (RTW).STS was significantly positively correlated with all other three traits.A total of 15 putative quantitative trait loci (QTLs) associated with these four traits were detected using single-point analysis,which were located on chromosomes 1,2,3,6,7,9 and 10 with 8％-26％ explaining the phenotypic variance.The O.rufipogon-derived alleles at 13 QTLs (86.7％) could improve the salt tolerance in the Teqing background.Four QTL clusters affecting RRW,RSW and RTW were found on chromosomes 6,7,9 and 10,respectively.Among these four QTL clusters,a major cluster including three QTLs (qRRW10,qRSW10 and qRTW10) was found near the maker RM271 on the long arm of chromosome 10,and the O.rufipogon-derived alleles at these three loci increased RRW,RSW and RTW with additive effects of 22.7％,17.3％ and 18.5％,respectively,while the phenotypic variance explained by these three individual QTLs for the three traits varied from 19％ to 26％.In addition,several salt tolerant ILs were selected and could be used for identifying and utilizing favorable salt tolerant genes from common wild rice and used in the salt tolerant rice breeding program.     

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.

     

Genetic analysis of salt stress responses in asparagus bean (Vigna unguiculata (L.) ssp. sesquipedalis Verdc.)

Salt stress responses of 23 asparagus bean cultivars were evaluated using 14-day-old seedlings after 15-day exposure to 75 mM NaCl in a hydroponics culture system. Salt-induced changes in plant growth and morphology, photosynthetic capacity, cell membrane integrity, and cellular protection enzyme systems as well as other physiological and biochemical traits were investigated to identify genotypic variability in salt response. This study also analyzed heredity parameters and correlation of the salt response index (SRI). Salt stress suppressed seedling growth and simultaneously reduced leaf area, content of chlorophyll and soluble proteins, net assimilation rate, as well as dry matter accumulation. In contrast, leaf blade cell membrane relative permeability, content of malondialdehyde, and antioxidant enzyme activity were elevated after salt treatment. Analysis of the heredity parameters has identified that the 18 investigated traits have different genotypic variance of the SRI values. Based on Ward's distances estimated for the sum of square variance in the SRI values, all the cultivars were classified into 2 discrete salt-tolerant and salt-sensitive clusters. Findings from this study will provide theoretical bases for identification and breeding of salt-tolerant cultivars in asparagus bean.     

Higher salinity tolerance cultivars of winter wheat relieved senescence at reproductive stage

In order to probe into the potential of relieving senescence in the new cultivars, we have compared gas exchanges and related physiological parameters of two cultivars of winter wheat (DK961, salt-tolerant; JN17, salt-sensitive) under a series of NaCl concentrations. Through out the whole reproductive period, it was noted that net photosynthetic rate, stomatal conductance, pigment contents, ions contents, leaf area index, leaf area duration, leaf relative water content and dry matter accumulation of spikes decreased in both cultivars with saline concentrations increasing. However, the salt-tolerant cultivars showed none significant reductions in those parameters compared with control under 0.3% and 0.5% salt concentrations, with only considerable decrease happening when soil salt concentration exceeded to 0.7%. Sharply contrast to salt-tolerant cultivars, the salt-sensitive cultivars appeared linear reductions in physiological parameters under a series of salt concentrations (0.3%, 0.5% and 0.7%), with the photosynthetic duration being evidently shorter. Significantly positive correlations among K⁺/Na⁺, reproductive growth period and total growth period were noted in salt-sensitive cultivars, however, none significant relations appeared among those parameters in salt-tolerant cultivars, indicating a strong tolerant behavior happened. Our result suggested that higher salinity tolerance cultivars of winter wheat could relieve senescence at the reproductive stage.     

Targeted association analysis identified japonica rice varieties achieving Na+/K+ homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra

During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these loci was extremely low, indicating a random distribution of favourable alleles in the ERCC. Analysis of the function of these loci indicated that all major tolerance mechanisms were present in the ERCC although the useful level of expression of the different mechanisms was scattered among different accessions. Under moderate salinity stress some accessions achieved the same level of control of Na(+) concentration and Na(+)/K(+) equilibrium as the indica reference variety for salinity tolerance Nona Bokra, although without sharing the same alleles at several loci associated with Na(+) concentration. This suggests (a) differences between indica and japonica subspecies in the effect of QTLs and genes involved in salinity tolerance and (b) further potential for the improvement of tolerance to salinity above the tolerance level of Nona Bokra, provided the underlying mechanisms are complementary at the whole plant level. No accession carried all favourable alleles, or showed the best phenotypic responses for all traits measured. At least nine accessions were needed to assemble the favourable alleles and all the best phenotypic responses. An effective strategy for the accumulation of the favourable alleles would be marker-assisted population improvement.     

Identification of <Emphasis Type="Italic">GmSALT3</Emphasis> haplotypes and development of molecular markers based on their diversity associated with salt tolerance in soybean

Soybean [Glycine max (L.) Merr.] is a major agricultural crop and generally known as a salt-sensitive crop. In a previous study, GmSALT3 was identified as a salt tolerance gene in soybean, and its nine haplotypes (H1 to H9) were reported in Chinese soybean accessions. In the present study, we aimed to identify new haplotypes of GmSALT3 in soybean accessions and to develop molecular markers for selection of salt-tolerant and -sensitive accessions. To do so, we examined genomic variations in the GmSALT3 coding region of 216 accessions of G. max and G. soja from Korea, China, and Japan. As a result, 40 different haplotypes, including three known haplotypes (H1, H2, and H5), were identified. Performing salt tolerance tests for the haplotypes, we were able to classify them into salt-tolerant (8) and salt-sensitive (32) categories. We also found that more variations in the haplotype composition of G. soja accessions exist than in that of G. max accessions. Quantitative expression analysis showed that almost all of the salt-tolerant haplotypes had much higher levels of GmSALT3 expression than the salt-sensitive haplotypes did. Finally, we developed molecular markers and applied them to screen salt tolerance of soybean accessions. The molecular markers performed well with an accuracy of 98.8% in identifying phenotypes of soybean accessions.