Identification of quantitative trait loci for grain yield, seed protein concentration and maturity in field pea (Pisum sativum L.)

Breeding efforts to improve grain yield, seed protein concentration and early maturity in pea (Pisum sativum L.) have proven to be difficult. The use of molecular markers will improve our understanding of the genetic factors conditioning these traits and is expected to assist in selection of superior genotypes. This study was conducted to identify genetic loci associated with grain yield, seed protein concentration and early maturity in pea. A population of 88 recombinant inbred lines (RILs) that was developed from a cross between 'Carneval' and 'MP1401' was evaluated at 13 environments across the provinces of Alberta, Manitoba and Saskatchewan, Canada in 1998, 1999 and 2000. A linkage map consisting of 193 AFLPs (amplified fragment length polymorphism), 13 RAPDs (random amplified polymorphic DNA) and one STS (sequence tagged site) marker was used to identify putative quantitative trait loci (QTL) for grain yield, seed protein concentration and early maturity. Four QTL were identified each for grain yield and days to maturity, and three QTL were identified for seed protein concentration. A multiple QTL model for each trait showed that these genomic regions accounted for 39%, 45% and 35% of the total phenotypic variation for grain yield, seed protein concentration and days to maturity, respectively. The consistency of these QTL across environments and their potential for marker-assisted selection are discussed in this report.     

Within and between genotypes variation in crude protein content of Phaseolus vulgaris L.

Summary A study of sources of variation in protein content within and between genotypes of Phaseolus vulgaris L. was carried out.The results show that bean to bean variation is large within a plant but that it is not due to systematic effects within pods or between nodes in determinate varieties. Pod to pod variation within nodes does occur. For indeterminate varieties, with large numbers of nodes, the protein content of seeds decreases with increasing node number from the base to the top of the plant. Plant to plant variation may be large, but depends on the genotype used. There is a large range of variability present within the species and selection for high protein content should be effective.     

Inter-relationships among total crude protein and digestible dry matter production and their component traits in Guinea grass

Summary Phenotypic and genotypic correlation coefficients of total crude protein per plant (TCP) and digestible dry matter per plant (DDM) with dry matter yield per plant (DMY), tiller number, plant height, stem thickness and leaf-stem ratio, pooled over two years, revealed that TCP and DDM were correlated at both the phenotypic and genotypic levels with DMY, tiller number and plant height. But only DMY had high direct effects on TCP and DDM. Tiller number and plant height had only indirect effects on TCP and DDM via DMY. Thus, selection based on tiller number and plant height may not only improve dry matter yield per plant but also total crude protein per plant and digestible dry matter per plant. Further, screening of high TCP and high DDM clones among the high yielding clones would be a more remunerative approach to improve TCP and DDM in Guinea grass.     

玉米开花期相关的Indeterminate domain(IDD)蛋白家族基因的鉴定

开花期是影响玉米产量的重要因子之一。Indeterminate1 (ID1)编码玉米Indeterminate domain (IDD)家族蛋白,是玉米开花期的重要调控因子。然而,其他玉米IDD蛋白家族基因及其生物学功能有待深入研究。本文利用生物信息学技术在玉米基因组中鉴定并分离了37个IDD家族基因,记作ZmIDD。表达分析发现这些ZmIDD基因在8个玉米组织中显示出多种表达模式。为进一步探讨ZmIDD基因在调控玉米开花期上的作用,检测了37个ZmIDD在172个自交系中的遗传多样性,发现35个ZmIDD基因在自交系间具有多态性,平均每个基因具有37.8个多态性位点。关联分析鉴定到包含ID1在内的7个ZmIDD基因在多个环境下与开花期性状显著关联。对Zm00001d020683基因2 kb的启动子区和600 bp编码区重测序,共鉴定到64个多态性位点。候选基因关联分析鉴定到2个启动子区的插入缺失(In/Del)位点与开花期显著关联,其中2个位点分别插入3 bp和2 bp的单倍型为一种提早开花的基因型。研究结果为玉米开花期相关基因的分离和利用研究提供了候选基因和选择靶点。     

A mutation in Waxy gene affects amylose content,starch granules and kernel characteristics of barley (Hordeum vulgare)

Waxy barley referred to as low‐amylose or amylose‐free has special advantages in nutrition composition and food processing. Waxy gene encoding granule–bound starch synthase I (GBSSI) is responsible for amylose synthesis in barley. The G³⁹³⁵‐to‐T in Waxy gene has been previously found in amylose–free barley. In this study, G³⁹³⁵‐to‐T was proved to co‐segregate with the waxy phenotype of barley, but has no obvious effect on GBSSI catalytic activity and starch chain length distribution. However, recombinant inbred lines with G³⁹³⁵‐to‐T in Waxy gene are of significant modification in starch granules morphology and pasting properties, increase of grain β‐glucan content, and decrease of thousand kernel weight along with lower kernel width. A polymerase chain reaction with confronting two–pair primers marker was developed for economic and efficient screening of G³⁹³⁵‐to‐T. This study provides the basis for cultivar improvement of waxy barley then fully developing its potential value and utility in food processing.     

Yield components,harvest index and plant type in relation to yield differences in field pea genotypes

Summary The effectiveness of yield components, harvest index and morphological characteristics as selection criteria among four field pea (Pisum sativum L.) genotypes was examined. Genotypes were grown at a wide range of plant populations (9 to 400 plants m^-2) to maximise environmental diversity.Both biological and seed yields approximately doubled from 9 to 100 plants m^-2. This response flattened from 100 to 400 plants m^-2. Differences among the genotypes were found only at 225 and 400 plants m^-2. Analysis of the yield components highlighted the plasticity and large genotype by environment interactions of field peas. The numbers of pods per plant and peas per pod were maximised when each genotype was grown as spaced plants, but the low plant numbers meant seed yields per unit area were at their lowest.Genotypic differences for plant harvest index (PHI) were also only found at 225 and 400 plants m^-2. Broad sense heritability estimates indicated that direct selection for PHI was not feasible. The inference from the yield component and PHI results was that alternative selection criteria such as physiological or morphological characteristics may be necessary for improved yield potential. Classification of each genotype indicated that low seedling vigour may be a positive attribute for crop plants of semi-leafless and conventionally leafed field peas. Selection based on any single plant attribute is unlikely to lead to dramatic improvements in the yield potential of field peas. Selection should be based on plant characteristics rather than on differences in yield components.     

Mapping quantitative trait loci for oil,starch, and protein concentrations in grain with high-oil maize by SSR markers

The objective of this investigation was to map QTL controlling oil, protein, and starch concentrations in maize grain and to evaluate their genetic effects. The mapping population included 298 F_2:3 family lines containing Beijing high-oil (BHO) maize germplasm. F₂ individuals were genotyped with 183 SSR markers to construct a genetic linkage map, which spanned 1,605.7 cM, with an average interval of 8.77 cM. Oil, protein, and starch concentrations in grain among F_2:3 families were measured by near-infrared (NIR) analyzer. Using QTL Cartographer, we mapped six QTL associated with oil in grain, six associated with protein, and five associated with starch concentrations. The proportion of phenotypic variation explained by single QTL ranged from 4.34 to 13.13% for oil, from 5.19 to 6.66% for protein, and from 4.14 to 7.85% for starch concentrations. QTL for oil, protein, or starch concentrations were often detected in identical intervals and the direction of their effects were consistent with the sign of their phenotypic correlation. They were considered as common QTL for chemical compositions in maize grain. In this study, we identified three QTL for oil in grain, two QTL for protein, and three QTL for starch concentrations, which were on identical or similar chromosomal locations to those previously mapped with Illinois high-oil (IHO) maize germplasm. These suggests that more diverse germplasm should be necessary to detect additional QTL and to discover more favorable alleles for chemical composition of maize grain.     

Diversity in starch, protein and mineral composition of sorghum landrace accessions from Ethiopia

Sorghum (Sorghum bicolor (L.) Moench) is an important food crop in arid and semi-arid tropics where it is grown mainly due to its drought tolerance. In Ethiopia, sorghum is grown in different agro-ecological zones primarily for food. Landraces are widely cultivated in the region due to their adaptation to the growing conditions and other characteristics such as food quality, quantity, and quality of by-products. The objective of this research was to determine the genetic variation in protein, mineral composition, total starch and its components in sorghum landraces collected from the western regions of Ethiopia. Sorghum whole grains were analyzed for crude protein, total starch and its components, and mineral profile (calcium, magnesium, potassium, phosphorus, iron, manganese, zinc, and sodium). The analysis of variance showed significant differences among the sorghum landraces in nutritional composition. There was highly significant correlation between phosphorus and magnesium, and between zinc and phosphorus and protein which indicated that some interaction existed in absorption and translocation between minerals and protein content. The genetic variation found among the sorghum landrace accessions in chemical composition can be exploited in the breeding program.     

Sequence variation in the barley genes encoding sucrose synthase I and sucrose phosphate synthase II,and its association with variation in grain traits and malting quality

Sequence diversity in the two barley (Hordeum vulgare L.) genes encoding sucrose synthase I (SSI) and sucrose phosphate synthase II (SPSII), both of which are involved in sucrose accumulation and grain filling, was studied by partial resequencing of eight reference genotypes and SNP analysis by pyrosequencing in a panel of 94 spring and 96 winter European barley varieties. The resequencing was based on two adjacent SSI fragments of size 880 and 820 bp, and a 2,322 bp SPSII fragment. In the SSI gene, 26 SNPs were present in the larger fragment, and 25 in the smaller one, and 11 of these were exploited to develop high-throughput SNP assays used for haplotype analysis. An association analysis based on either a general or a mixed linear model suggested that the predominant three haplotypes influenced certain components of both kernel and malting quality. However, the level of phenotype/haplotype association shown with the SPSII gene was rather low. SNP variation of SSI was used to map the locus to chromosome 7H.     

Waxy proteins and amylose content in diploid Triticeae species with genomes A, S and D

A collection of 89 accessions of diploid species of wheat was analysed for waxy protein in the grain: 39 accessions of Einkorn wheats, 41 accessions of Sitopsis section wheat and nine accessions of Triticum tauschii. The electrophoretic patterns showed low polymorphism. In each group of wheat, a single and different allele was detected. In accessions of Einkorn wheats that allele had a similar electrophoretical mobility to the Wx‐A1a allele of the bread wheat ‘Chinese Spring’, in accessions of the Sitopsis section it had a similar mobility to that of the Wx‐B1f allele of tetraploid wheat, and in the accessions of T. tauschii, it was similar to the Wx‐D1a allele of the bread wheat ‘Chinese Spring’. The accessions were also analysed for apparent amylose content. Results showed that amylose content ranged from 22 to 35% in Einkorn wheats, from 28 to 41% in the Sitopsis section and from 26 to 35% in accessions of T. tauschii.     

Waterlogging differentially affects yield and its components in wheat,barley, rapeseed and field pea depending on the timing of occurrence

Waterlogging on croplands is increasing in various areas of the world. This study evaluated the yield penalty by early and late waterlogging on wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rapeseed (Brassica napus L.) and field pea (Pisum sativum L.). Plants cultivated outdoors were exposed to a 14-day waterlogging during vegetative (at 65 days after sowing (DAS)) or reproductive (at 85/87 DAS) stages, followed by drained conditions until maturity. Yield (seed weight per plant) and its components (number of spikes/siliques/pods per plant, number of grains per spike/silique/pod and 1,000 grain weight) were assessed at maturity, along with morphological (number of tillers/branches) and shoot and root dry weight responses after waterlogging and during recovery. Wheat was the most tolerant species achieving 86% and 71% of controls in yield with early and late waterlogging, related to fewer grains per spike. Barley and rapeseed tolerated early waterlogging (yields 85% and 79% of controls) as compared to late waterlogging (32% and 26% of controls), mainly due to fewer spikes per plant (barley) or reductions in seeds per silique (rapeseed). Field pea was greatly affected by waterlogging at both timings, attaining a yield of only 6% of controls on average due to much fewer pods and fewer seeds per pod. So, wheat could be an option for areas facing either winter or spring transient waterlogging (i.e. early or late stages); barley and rapeseed are recommended only with if water excess occurs in early stages and field pea is intolerant to waterlogging.     

Origin and variation of gliadin proteins associated with pasta quality in durum wheat

Summary Studies were made of the presence and frequency of occurrence of gliadin bands 42 and 45 in three samples of Aegilops sharonensis Eig and 59 samples of wild tetraploid wheat (Triticum dicoccoides Korn.) from natural distributions of these species in Israel.Two samples of Ae. sharonensis possessed a band in position 45 and one possessed no bands corresponding to either band 45 or band 42. In T. dicoccoides, band 45 was either present or not and 42 was always absent. In its grassy and intermediate growth habit forms, (believed to be more primitieve than the cercal forms) band 45 appeared to be more frequent than in the cereal form.The presence of band 45 in the Ae. sharonensis, and its relatively high frequency in T. dicoccoides, populations from Mt. Hermon (likely to be relatively free from introgression from cultivated tetraploid wheat) indicate the likelihood of a primary origin of the allele coding for band 45. The absence of band 42 from all Ae. sharonensis and T. dicoccoides populations in this study, indicates a more recent evolutionary origin of the allele coding for this band, possibly arising as a mutation during the domestication of tetraploid wheat.The results have implications for breeding programmes in tetraploid wheat.     

Identification of QTLs associated with metribuzin tolerance in field pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

Competition with weeds is a major constraint to production of field pea in Australia, exacerbated by limited herbicide control options. Metribuzin is considered to be a safe herbicide, but may be phytotoxic to both weeds and target crop. A preliminary glasshouse-based assay was used to identify the optimal concentration required for discrimination between tolerant and sensitive field pea genotypes as 10 ppm metribuzin. This dosage was subsequently used to screen the Kaspa × PBA Oura recombinant inbred line genetic mapping population of 185 individuals for tolerance to metribuzin in three individual controlled environment assays. After two weeks of metribuzin treatment, plants were assessed on the basis of both a numerical score for symptoms such as chlorosis and necrosis, and plant damage as a percentage of necrosis. The two phenotypic parameters showed a high level of correlation (r = 0.85–0.97). The locations and magnitudes of effect of quantitative trait loci (QTLs) were determined for metribuzin tolerance (based on both symptom score and plant damage) as well as several related morphological traits. Analysis of all characters detected a single genomic region located on linkage group (LG) Ps IV (LOD scores 3.5–5.7), accounting for proportions of phenotypic variance for plant symptom score and percentage of plant necrosis varying from 12 to 21%. Genetic markers based on genic sequences that closely flank the metribuzin tolerance QTL are suitable for implementation in field pea breeding programs. In addition, comparative genomics between field pea and Medicago truncatula identified a cytochrome P450 monooxygenase gene in the vicinity of the QTL, potentially involved in non-target-site metabolism-based herbicide tolerance.     

Low temperature induced changes in activity and protein levels of the enzymes associated to conversion of starch to sucrose in banana fruit

Storage at low temperature is the most frequently used method to extend the shelf life of banana fruit, and is fundamental for extended storage and transport over long distances. However, storage and transport conditions must be carefully controlled because of the high susceptibility of many commercial cultivars to chilling injury. The physiological behavior of bananas at low temperatures has been studied to identify possible mechanisms of resistance to chilling injury. The aim of this work was to evaluate differences in the starch-to-sucrose metabolism of a less tolerant and susceptible (Musa acuminata, AAA cv. Nanicão) and a more tolerant (M. acuminata × Musa balbusiana, AAB, cv. Prata) banana cultivar to chilling injury. Fruits of these cultivars were stored in chambers at 13 °C for 15 d, at which point they were transferred to 19 °C, where they were left until complete ripening. The low temperature induced significant changes in the metabolism of starch and sucrose in comparison to fruit ripened only at 19 °C. The sucrose accumulation was slightly higher in cv. Prata, and different patterns of starch degradation, sucrose synthesis, activity and protein levels of the α- and β-amylases, starch phosphorylase, sucrose synthase and sucrose phosphate synthase were detected between the cultivars. Our results suggest that starch-to-sucrose metabolism is likely part of the mechanism for cold acclimation in banana fruit, and the cultivar-dependent differences contribute to their ability to tolerate cold temperatures.     

A high-throughput, low cost gel-based SNP assay for positional cloning and marker assisted breeding of useful genes in cereals

Several SNP (single nucleotide polymorphism) genotyping methods have been developed in the past most of which require sophisticated instrumentation and large initial investments. We describe here a high-throughput SSCP (single strand conformation polymorphism) system on our HEGS (high efficiency genome scanning) platform, which is simple, accurate, cost effective and requires neither restriction digestion of the amplification products nor elaborate post-PCR processing detection. Several parameters critical to SSCP analysis were optimized viz., gel matrix and concentration, gel running temperature, buffer composition, running conditions and PCR primer design so as to identify SNPs in amplicons ranging from 100 to 750 bp in size. A simple post-PCR processing system was developed using fluorescent dye for quick and easy detection of SNP polymorphism. HEGS-SSCP was also found to be useful in uncovering simple sequence repeat differences between different genotypes that differ by one or few di/tri nucleotide repeats. The practical utility of this system is illustrated with two successful efforts towards construction of high resolution linkage maps of a lesion mimic locus on chromosome 7 and a major quantitative trait locus conditioning field blast resistance on chromosome 4 in rice.     

In vitro protein digestibility in grain sorghum: effect of genotype and interaction with starch digestibility

Improvement of nutritive value is one of the main goals of sorghum breeding. It is known that one of the reasons of relatively poor nutritive value of sorghum grain is resistance of its seed storage proteins (kafirins) to protease digestion that also affects digestibility of starch. To study genetic aspects and interdependency of these traits we investigated in vitro protein and starch digestibility of the flour of 12 grain sorghum lines and six F₁ hybrids. Comparison of SDS-PAGE spectra of total grain proteins before and after pepsin digestion revealed that the F₁ hybrids had significantly lower indices of protein digestibility than parental lines, with the exception of the F₁ hybrid M35-1A KB/KVV-45, which retained high level of protein digestibility typical for KVV-45 line. The level of starch digestibility in the F₁ hybrids corresponded to its level in maternal lines suggesting importance of maternal genotype in determination of this trait. It was found that starch digestion by amylolytic enzymes increased the amount of protein in individual kafirin fractions, and reduced the amount of high molecular weight proteins as well it reduced subsequent kafirin digestion by pepsin and caused formation of polypeptide (M_r ~45 kDa), perhaps, the kafirin dimer, resistant to pepsin digestion. These data are of importance for fundamental investigation of factors influencing kafirins and starch interactions in sorghum endosperm and their digestibility.     

Identifying and exploring significant genomic regions associated with soybean yield,seed fatty acids,protein and oil

Soybean [Glycine max (L.) Merrill] yield and seed fatty acids, protein, and oil content are important traits for which an improved understanding of significant genomic regions would be useful. To accomplish this, a soybean population consisting of 203 F5 derived recombinant inbred lines (RILs) was developed and genotyped with 11,633 polymorphic single nucleotide polymorphisms (SNPs). Each RIL was grown in a single plot at Knoxville, TN in 2010; followed by replicated, multi-location field trials in 2013 and 2014. The data from 2010, 2013, and 2014 were analyzed together in order to detect quantitative trait loci (QTL) for these traits, and 30 total QTLs were detected. Five QTLs are candidates for confirmed status and one QTL is a candidate for positional confirmation. Many of the genes with mutations in close proximity to the fatty acid QTLs are involved in biological processes for fatty acids and/or lipids and could be considered possible candidate genes. Similarly, genes with mutations in genomic regions near yield, protein, and oil QTLs were plentiful and may contribute to the variation observed in these traits. Except for yield and stearic acid, each trait displayed pleiotropic effects with other traits in this study. Notable are the pleiotropic effects for oleic and linolenic acid on chromosomes 9, 13, and 19. Overall, the findings from this research contribute new information to the genetic understanding of soybean yield and seed fatty acids, protein and oil content. This understanding will be useful in making trait improvements.