Genome mapping and molecular markers identification for yield,yield component and fibre quality traits in tetraploid cotton

The identification of quantitative trait loci (QTL) across different environments is a prerequisite for marker‐assisted selection (MAS) in crop improvement programmes. CottonSNP63k Illumina infinium array was used for genotyping 178 inter‐specific recombinant inbred lines and the parents, and identified 1,667 homozygous polymorphic markers between the parents. Of these, 1,430 markers were used for the construction of linkage map after removing 237 redundant markers. The genetic map spans a total genetic length of 3,149.8 cM with an average marker interval size of 2.2 cM. The phenotypic data from five environments were analysed separately using inclusive composite interval mapping which identified a total of 56 QTL explaining phenotypic variances (PVE) in the range of 8.18%–28.91%. There were 11 and 24 major QTL found for fibre quality and yield components, respectively. A total of 64 QTL were identified through Multi‐Environment Trials analysis, of which 34 recorded QTL × Environment interactions.     

越冬栽培稻产量性状相关QTL定位

越冬栽培稻是一类能越过自然冷冬季节并在第2年春季萌芽、正常开花结实、收获稻谷的水稻品种。本文通过对越冬栽培稻产量性状QTL分析,明确产量相关性状的遗传规律,旨在进一步解析越冬栽培稻产量性状的遗传机制,为育种创新利用提供理论依据。以3份越冬栽培稻构建的3个半同胞F2群体为材料。各考察15个产量相关性状,利用Excel 2003、GraphPad Prism 5.0和QTL IciMapping 4.10软件分析数据、绘制遗传图谱、定位QTL和联合分析。结果表明,产量性状表型值在3群体中呈连续正态分布,表现为数量性状遗传。共检测到37个QTL和26对上位性QTL,贡献率分别介于2.32%～36.31%和1.04%～2.05%;检测到9个同时影响2个及以上产量性状(一因多效)QTL标记区间;以联合分析检测到13个产量性状相关QTL,其中4个QTL区间与单群体检测QTL区间重叠;越冬栽培稻产量相关性状QTL以加–显性效应遗传为主、上位性遗传效应为辅。本研究将为越冬栽培稻产量相关基因挖掘及育种创新利用奠定基础。     

Genome-wide association study of yield components and fibre quality traits in a cotton germplasm diversity panel

A genome-wide association study (GWAS) was conducted on a diversity panel of 103 cotton accessions over three seasons to determine genetic contributions to a range of cotton yield components including fibre quality, plant architecture and stomatal conductance traits. The accessions covered breeding lines, released cultivars and some obsolete cultivars that contributed significantly to modern breeding pools. They were genotyped with Illumina’s CottonSNP63 K single nucleotide polymorphism (SNP) assay. Broad-sense heritability was low for yield component traits (\(h_{B}^{2}\) = 0.14–0.43), except for gin turnout and boll weight (\(h_{B}^{2}\)) = 0.74 and 0.59, respectively), and low to high for fibre quality traits (\(h_{B}^{2}\) = 0.26–0.89). Population structure analysis revealed extensive admixture and cryptic relatedness amongst the accessions. Genome-wide linkage disequilibrium (LD) analyses showed LD decayed, on average, within a physical distance of 5 Mbp and reduced to 2 Mbp at r ² ≥ 0.2, suggesting that few markers are necessary for association mapping in cotton. A mixed linear model accounting for population structure and cryptic relatedness identified 17 and 50 significant SNP associations for fibre length and micronaire, respectively. GWAS failed to detect significant associations in other traits, with the contribution of any single SNP to the phenotypic falling below 5%. This may be due to the low level of DNA polymorphism in cotton and/or insufficient resolution provided by the cotton SNP chip. Whole genome sequencing combined with whole genomic selection approaches that do not require prior knowledge about the effect or function of individual SNPs may be better suited than GWAS for trait dissection and prediction in cotton breeding.     

Association mapping for seed cotton yield,yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

Association mapping has revolutionized human genetics and is increasingly used in plant genetics. It is an efficient way of determining the genetic basis of complex traits. In cotton so far numerous association mapping studies are available as compared to many other important crops. In our study, mapping was performed using cotton 63K infinium beadchip with 201 germplasm lines. Through fast STRUCTURE analysis, lines were grouped into 12 subgroups and revealed genome sharing among the groups. The critical value (R²) was set to 0.243 as threshold to claim LD between two loci. About 3.13% marker pairs recorded significantly high LD (R² = 1), and 8.19% of marker pairs were in the range of 0.3 to 0.99 R². In MLM, 349 significant marker–trait associations were detected as against 642 in GLM because of effectiveness in eliminating false associations in MLM. A total of 68 markers explained >10% phenotypic variation for yield and fibre quality traits. Phenotypic variation explained by markers was smaller, suggesting that they might be associated with minor QTLs.     

Breeding for high yield and fibre quality in coloured cotton

In the present study, three types of coloured fibre cottons, i.e. white, brown and green, were compared for their fibre quality and yield. The comparison of fibre quality suggested that coloured fibre cotton was inferior as compared with white fibre cotton. To understand the effect of cellulose, mineral elements [nitrogen (N), phosphorus (P) and potassium (K)] and pH of fibre cells on the quality of fibre, these components were studied at different fibre cell developed stages in all three fibre cotton types. The cellulose content is closely associated with the quality of fibre. The higher fibre quality of white fibre cotton might be the result of the high cellulose content in it compared with coloured fibre cotton. A rapid and slow decrease in pH in white and coloured cottons, respectively, might have some effects on fibre elongation. Among the mineral contents, potassium is positively correlated with the fibre quality traits. The pigment development patterns in brown and green fibre cottons are not similar. In green fibre cotton it takes more time to deepen in colour as compared with brown fibre cotton. Possible strategies for the improvement in quality of coloured fibre cotton are discussed. The results of heterosis studies in coloured fibre cotton suggest that heterosis could improve yield and quality of coloured fibre cotton. In the present study, the hybrids between ZJU12A x ZJU05R and ZJU18A x ZJU01R, having an acceptable lint colour types plus better fibre quality and high yield performance, may be exploited further for their heterotic advantages.     

A preliminary genetic analysis of fibre traits and the use of new genomic SSRs for genetic diversity in jute

Jute is one of the most important fibre crops, which is second only to cotton in providing environment-friendly (biodegradable and renewable) ligno-cellulose fibre. In order to improve this largely neglected crop, we conducted a preliminary study involving the following: (i) analysis of nature and extent of the genetic variability for fibre yield and four other related traits in a set of 81 genotypes belonging to two commercially cultivated Corchorus species (45 genotypes of C. olitorius + 36 genotypes of C. capsularis), (ii) development and analysis of a set of simple sequence repeat (SSR) markers from C. olitorius, and (iii) use of a sub-set of SSRs for assessment of genetic diversity in the above set of 81 genotypes. The results suggested quantitative nature of fibre yield and other related traits, with a preponderance of dominance component in genetic variance. A sub-set of 45 SSRs derived from C. olitorius, when used for a study of DNA polymorphism and genetic diversity, showed high transferability of these C. olitorius SSRs to C. capsularis. The average number of alleles for individual SSRs was surprisingly low (3.04 for both species, 2.02 for C. capsularis and 2.51 for C. olitorius), and so was the average polymorphic information content (PIC; 0.23 and 0.24 in two species). In the dendrogram obtained using a similarity matrix, the 81 genotypes were grouped into three clusters, which largely corresponded to the two species, Cluster I belonging mainly to C. capsularis and the other two closely related clusters (clusters II and III) belonging to C. olitorius. It was also shown that a minimum of 15 SSRs could give the same information as 41 SSRs, thus making many SSRs redundant. The SSR markers developed during the present study and to be developed in future will prove useful not only for evaluation of genetic diversity, but also for molecular mapping/QTL analysis, and for comparative genome analysis of the two Corchorus species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Combining ability for seed yield traits of Chenopodium quinoa breeding lines

For a better understanding of the inheritance of seed yield traits in Quinoa (Chenopodium quinoa) Willd., a half-diallelic crossing experiment with six diverse but uniform breeding lines was conducted. True hybrid plants were detected by means of differences in panicle colour in 14 out of the 15 crosses performed. The agronomic performance of 14 F₂ populations and six parental lines was evaluated in field trials on fertile clay soil. General and specific combining ability of the lines (GCA and SCA) were estimated. Highly significant differences in GCA effects were found between the lines for plant height at maturity, early flowering, early maturity, seed yield and thousand seed weight. Significant SCA effects were only found for plant height at maturity. However, SCA effects were rather small and accounted for 7% of the total variance. The finding of large GCA effects and low SCA effects suggests that best selection results could be expected from crosses between the agronomic best performing genotypes. This revised version was published online in August 2006 with corrections to the Cover Date.     

黄麻SSR标记与纤维产量性状的相关性

Simple sequence repeat (SSR) markers correlated to fiber yield traits would be a beneficial tool for molecular marker-assisted breeding in jute. In this study, 397 SSR markers were screened from 311 jute germplasms by the phenotype identification from 2016 to 2018 and 116 pairs of primers. The correlation analysis between SSR markers and fiber yield related traits by SPSS revealed that the range of the coefficient of variation related to 9 fiber traits was from 13.05% to 76.78%, indicating a comprehensive genetic variation. The correlation analysis of the agronomic traits showed that there were significantly correlations among these traits. The average correlation coefficient between branch height and nodes of main stem was the highest (r = 0.931), followed by the correlation coefficients (r = 0.781) of fresh bark weight per plant and fresh stem weight per plant and the coefficients (r = 0.779) of dry bark weight and fresh bark weight per plant. Analysis of variance (ANOVA) showed that the traits of main stem nodes, number of branches, plant height and branch height were relatively stable in different years with the higher broad heritability capacity. Furthermore, the SSR markers associated with fiber yield related traits were identified by Pearson correlation method. Stepwise regression analysis among each trait associated SSR markers indicated that there were six markers associated significantly with fiber yield related traits, and phenotypic variation explained by each SSR marker varied from 3.9% to 22.5%. These results will accelerate the development of molecular design breeding in jute.     

Genetic and QTL analyses of yield and a set of physiological traits in pepper

An interesting strategy for improvement of a complex trait dissects the complex trait in a number of physiological component traits, with the latter having hopefully a simple genetic basis. The complex trait is then improved via improvement of its component traits. As first part of such a strategy to improve yield in pepper, we present genetic and QTL analyses for four pepper experiments. Sixteen traits were analysed for a population of 149 recombinant inbred lines, obtained from a cross between the large-fruited pepper cultivar ‘Yolo Wonder’ (YW) and the small fruited pepper ‘Criollo de Morelos 334’ (CM334). The marker data consisted of 493 markers assembled into 17 linkage groups covering 1,775 cM. The trait distributions were unimodal, although sometimes skewed. Many traits displayed heterosis and transgression. Heritabilities were high (mean 0.86, with a range between 0.43 and 0.96). A multiple QTL mapping approach per trait and environment yielded 24 QTLs. The average numbers of QTLs per trait was two, ranging between zero and six. The total explained trait variance by QTLs varied between 9 and 61 %. QTL effects differed quantitatively between environments, but not qualitatively. For stem-related traits, the trait-increasing QTL alleles came from parent CM334, while for leaf and fruit related traits the increasing QTL alleles came from parent YW. The QTLs on linkage groups 1b, 2, 3a, 4, 6 and 12 showed pleiotropic effects with patterns that were consistent with the genetic correlations. These results contribute to a better understanding of the genetics of yield-related physiological traits in pepper and represent a first step in the improvement of the target trait yield.     

QTL mapping for agronomic and fibre traits using two interspecific chromosome substitution lines of Upland cotton

CS‐B14Sh and CS‐B22Sh are cotton interspecific chromosome substitution (CS)‐B lines, in which a pair of short arms of chromosome 14 and chromosome 22 were introgressed from Gossypium barbadense doubled‐haploid line 3‐79 with the background of Gossypium hirsutum line TM‐1, respectively. These two CS‐B lines were crossed with TM‐1, and segregating progenies (F₂ and F_2:3, respectively) were obtained. Phenotypic data of lint yield, yield‐related traits and fibre‐quality traits were collected from two trials. In the cross CS‐B14SH X TM‐1, QTL for boll weight (BW), lint percentage (LP), fibre upper half mean length (UHML), micronaire reading (MIC), and fibre breaking tensile strength (STR) were repeatedly detected. Alleles from 3‐79 decreased BW and MIC, but increased UHML and STR. In the cross CS‐B22Sh X TM‐1, QTL for BW, LP, UHML, MIC, STR, fibre elongation (EL),seed weight(SW), node of first fruiting branch (NFB) and fibre uniformity index (UI) were repeatedly detected, and alleles from 3‐79 decreased UHML, UI and STR, but increased NFB, SW, MIC and EL. QTL clusters were found in both populations.     

Agronomical and quality traits of runner bean germplasm and implications for breeding

White runner bean landraces are greatly appreciated in the North highlands of Spain due to their excellent culinary seed quality. Runner bean cultivars are grown like pole beans. Diversity within a runner bean collection of 31 accessions from the Iberian Peninsula (Spain and Portugal) was examined using morphological, agronomical and seed quality traits. Landraces showed significant differences for most of the agronomical and seed quality traits studied except for seeds per pod, water absorption, seed coat tenderness and floury texture. Runner bean landraces showed sufficient variability to select inbred lines for future breeding. Genotype × environment interaction was significant for days to first flowering, days to first dry pod, seeds per pod and seed length. The majority of physical and nutritional seed quality traits studied which are important to determine the commercial value of a variety were not subject to environmental influences. Different selection pressures affecting to the runner bean genetic material could have occurred in several regions of the Iberian Peninsula. Extra-large and high yielding runner bean germplasm was identified and represents a valuable source of genetic diversity that has potential for development of improved cultivars to be chosen for commercialisation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparison of stability statistics for yield and quality traits in bread wheat

The stability and genotypic mean of four traits, grain yield, grain protein content, alveograph W and bread volume, were evaluated in three multi-location trials, each covering two years. The stability of each genotype was evaluated by environmental variance (s² _E), interaction variance (s² _W) and variance of the ranks of the phenotypic values corrected for the genotypic effect (s² _R). The bootstrap method was used to study correlations between the genotypic mean and the three stability statistics and to calculate their accuracy. The repeatability of the stability statistics was measured by correlations between the values obtained in each of the two years. In addition, theoretical smaller trials were generated by random sampling and the stability values calculated were correlated with those of the original trial. Environmental variance appears to be usable both for yield and for quality traits, but there is a risk of counter-selecting a high genotypic mean of W. Whatever the trait and statistic envisaged, stability is poorly repeatable and its evaluation requires several years and a large number of locations per year to minimise sampling and environmental effects. This revised version was published online in August 2006 with corrections to the Cover Date.     

A QTL atlas for grain yield and its component traits in maize (Zea mays)

Grain yield and its component traits are essential targets in maize breeding. These traits are genetically complex and controlled by a large number of quantitative trait loci (QTL). The aim of this study was to compile reported QTL and major genes for grain yield and its component traits in a QTL atlas, as a valuable resource for the maize community. To this end, 1,177 QTL related to maize yield were collected from 56 studies published between 1992 and 2018. These QTL were projected to genetic map “IBM2 2008 Neighbors”, which led to the identification of 135 meta-QTL. Some genomic regions appear to be hotspots for yield-related meta-QTL, often affecting more than one of the investigated traits. Moreover, we catalogued 20 major maize loci associated with yield and identified 65 maize homologs of 21 rice yield-related genes. Interestingly, we found that a significant proportion of them are located in meta-QTL regions. Collectively, this study provides a reference for QTL fine-mapping and gene cloning, as well as for molecular marker-assisted breeding of yield-related traits in maize.     

QTL identification of yield-related traits and their association with flowering and maturity in soybean

Two soybean recombinant inbred line populations, Jinpumkong 2 × SS2-2 (J × S) and Iksannamulkong × SS2-2 (I x S) showed population-specific quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) and these were closely correlated within population. In the present study, we identified QTLs for six yield-related traits with simple sequence repeat markers, and biological correlations between flowering traits and yield-related traits. The yield-related traits included plant height (PH), node numbers of main stem (NNMS), pod numbers per plant (PNPP), seed numbers per pod (SNPP), 100-seed weight (SW), and seed yield per plant (SYPP). Eighteen QTLs for six yield-related traits were detected on nine chromosomes (Chrs), containing four QTLs for PH, two for NNMS, two for PNPP, three for SNPP, five for SW, and two for SYPP. Two highly significant QTLs for PH and NNMS were identified on Chr 6 (LG C2) in both populations where the major flowering gene, E1, and two DF and DM QTLs were located. One other PNPP QTL was also located on this region, explaining 12.9% of phenotypic variation. Other QTLs for yield-related traits showed population-specificity. Two significant SYPP QTLs potentially related with QTLs for SNPP and PNPP were found on the same loci of Chrs 8 (Satt390) and 10 (Sat_108). Also, highly significant positive phenotypic correlations (P < 0.01) were found between DF with PH, NNMS, PNPP, and SYPP in both populations, while flowering was negatively correlated with SNPP and SW in the J × S (P < 0.05) and I × S (P < 0.01) populations. Similar results were also shown between DM and yield-related traits, except for one SW. These QTLs identified may be useful for marker-assisted selection by soybean breeders.     

Root architectural traits and yield: exploring the relationship in barley breeding trials

Root system architecture is fundamental to resource capture and productivity of cereal crops. Understanding the genetics modulating root development will empower plant breeders to design cultivars with optimal root systems for the target environment. Here, we investigate the genetic association between seminal root traits and yield in elite barley (Hordeum vulgare L.) germplasm. A panel of 216 breeding lines from the Northern Region Barley Breeding program in Australia, genotyped with Diversity Arrays Technology markers, were characterised for seminal root angle and number. A high degree of phenotypic variation was evident in the population, ranging from 12.0° to 89.4° and 4.8 to 6.1 for root angle and number, respectively. A quantitative trait locus for root angle (qRA-5) was detected on chromosome 5H and co-located with the previously described RAQ2. The genetic relationship between seminal root traits and yield for the panel was investigated using root phenotypes and yield data from 20 field trials. Genetic correlations with yield ranged from ??0.21 to 0.36 for root angle and from ??0.20 to 0.25 for root number. The direction and magnitude of the correlations for both root traits varied across the environments, but overall root angle was deemed more strongly associated with yield. Here we provide insight into the root phenotypes of breeding lines and deliver a first look at the genetic relationship between root architectural traits and yield in barley breeding trials.     

Combining ability estimates for yield and fibre quality traits in 4 × 13 line × tester crosses of Gossypium hirsutum

The aim of this study was to estimate the general combining ability of the parents and specific combining ability of hybrids considered for the development of high yielding and better quality cultivars. Seventeen genotypes and 52 F₁ hybrids obtained by crossing 4 lines and 13 testers in line × tester mating system during 2003 were sown in randomized complete block design in 2004. Line × Tester analysis revealed significant GCA and SCA effects for all the traits except fibre elongation. Preponderance of non-additive gene action was obtained for seed cotton yield per␣plant and majority of its component traits including fibre traits. Among the parents: PIL-8 for days to 50% flowering, CCH-526612 for boll weight, CITH-77 for number of open bolls per plant and CNH-36 for seed cotton yield per plant were detected with higher general combining ability. Parent, CCH-526612 for 2.5% span length, fibre strength and fibre elongation and AKH-9618 for micronaire value, fibre strength and fibre elongation were good combiners for fibre quality traits. The F₁s achieved high seed cotton yield by producing more number of open bolls. The high yielding hybrids with acceptable fibre quality traits were: CISV-24 × LH-1995, H-1242 × PIL-8 and RS-2283 × SGNR-2 deducted with significant SCA effects for seed cotton yield and fibre characteristics; 2.5% span length and fibre strength. These cross combinations involved at least one parent with high or average GCA effect for a particular trait.     

Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD

Tetraploid cotton is one of the most extensively cultivated species. Two tetraploid species, Gossypium hirsutum L. and G. barbadense L., dominate the world's cotton production. To better understand the genetic basis of cotton fibre traits for the improvement of fibre quality, a genetic linkage map of tetraploid cotton was constructed using sequence‐related amplified polymorphisms (SRAPs), simple sequence repeats (SSRs) and random amplified polymorphic DNAs (RAPDs). A total of 238 SRAP primer combinations, 368 SSR primer pairs and 600 RAPD primers were used to screen polymorphisms between G. hirsutum cv. Handan208 and G. barbadense cv. Pima90 which revealed 749 polymorphic loci in total (205 SSRs, 107 RAPDs and 437 SRAPs). Sixty‐nine F₂ progeny from the interspecific cross of ‘Handan208’בPima90’ were genotyped with the 749 polymorphic markers. A total of 566 loci were assembled into 41 linkage groups with at least three loci in each group. Twenty‐eight linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 5141.8 cM with a mean interlocus space of 9.08 cM. A × test for significance of deviations from the expected ratio (1: 2: 1 or 3: 1) identified 135 loci (18.0%) with skewed segregation, most of which had an excess of maternal parental alleles. In total, 13 QTL associated with fibre traits were detected, among which two QTL were for fibre strength, four for fibre length and seven for micronaire value. These QTL were on nine linkage groups explaining 16.18‐28.92% of the trait variation. Six QTL were located in the A subgenome, six QTL in the D subgenome and one QTL in an unassigned linkage group. There were three QTL for micronaire value clustered on LG1, which would be very useful for improving this trait by molecular marker‐assisted selection.     

Status and perspectives of breeding for enhanced yield and quality of oilseed crops for Europe

Vegetable oils are a high-value agricultural commodity for use in refined edible oil products and as renewable industrial or fuel oils, and as the world population increases demand for high-quality seed oils continues to grow. Worldwide the oilseed market is dominated by soybean (Glycine max), followed by oilseed rape/canola (Brassica napus). In Europe the major oilseed crop is oilseed rape (B. napus), followed some way behind by sunflower (Helianthus annuus) and other minor crops like linseed (Linum usitatissimum) or camelina (Camelina sativa). The seed oil of these crops is characterized by a specific quality, i.e. fatty acid composition and other fat-soluble compounds: Camelina and linseed oils are characterised by high contents of linolenic acid (C18:3); in sunflower very high-oleic (up to 90% C18:1) types exist in addition to classical high-linoleic (C18:2) oilseeds; in B. napus a broad diversity of oil-types is available in addition to the modern 00 (canola) type, e.g. high-erucic acid rapeseed or high-oleic and low-linolenic cultivars. Moreover, vegetable oils contain valuable minor compounds such as tocopherols (vitamin E). Increases of such contents by breeding have lead to value-added edible oils. After oil extraction, oilseed meals—such as rapeseed extraction meal—contain a high-quality protein that can be used as a valuable animal feed. However, in comparison to soybean the meal from oilseed rape also contains relatively high amounts of anti-nutritive fibre compounds, phenolic acids, phytate and glucosinolates. Breeding efforts with respect to meal quality are therefore aimed at reduction of anti-nutritive components, while increasing the oil content, quality and yield also remains a major aim in oilseed rape breeding. This review article provides a general overview of the status of oilseed production in Europe and uses examples from winter oilseed rape to illustrate key breeding aims for sustainable and high-yielding production of high-quality vegetable oil. Emphasis is placed on analytical tools for high-throughput selection of overall seed quality.