Fiber Yield Traits Research Articles

Genetic Diversity of Ramie (Boehmeria Nivea L. Gaudich.) Originating from Wonosobo and Malang Based on Simple Sequence Repeat (SSR) Molecular Markers

Ramie has been widely used as a fiber crop for over 4000 years. The fibers are durable, white in color, and smooth in texture. Information on genetic diversity is important for selecting good breeding materials to produce superior offspring. This study aimed at determining the genetic diversity of Boehmeria nivea (L.) Gaudich. from Wonosobo and Malang using SSR as molecular markers. Nineteen accessions of ramie were analyzed for genetic diversity using 9 SSRs located adjacent to the gene associated with fiber yield traits. This study included the DNA extraction, amplification, and visualization of amplification. Data analysis included the allele number, frequency, PIC value, heterozygosity, Shannon information index, and AMOVA analysis. The results showed 229 alleles, with an average polymorphic percentage of 68.67%, the average allele frequency ranging from 0.07 to 0.11, an average PIC value of 0.84, and Jaccard's similarity score of 0-0.18. The He and Ho values in both populations were 0.719 and 0.278, respectively. AMOVA analysis revealed that 88% of the observed molecular variance was due to genetic differences within the population, whereas 12% of genetic variation was partitioned between populations. The present study showed high genetic diversity between Wonosobo and Malang ramie. This finding might support further programs for the fiber and biomaterial industry.

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.).

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

High-resolution genetic map construction and QTL analysis of important fiber traits in kenaf using RAD-seq

Kenaf fiber extracted from kenaf stem bast is an important natural fiber. The genetic basis of fiber yield and quality is poorly understood. In the present study, Fiber yield and quality phenotypic data showed continuous positive distribution or positively skewed distribution. Fiber yield traits and its related traits including plant height, fresh bast weight, dry bast weight showed a positive correlation. However, there was a negative correlation between fiber weight and fiber count. The results showed that the fiber yield and quality agronomic traits are quantitative traits controlled by multiple genes. Quantitative trait locus (QTL) mapping is a useful method for revealing the mechanism of complex genetic traits and identifying new genomic information to accelerate crop improvement. In this study, a total of 1,997 polymorphic SNP markers were successfully mapped onto 18 different linkage groups. Meanwhile six QTLs were identified based on the genetic map using the multiple QTL mapping (MQM) method, which were assigned to three linkage groups, LG16, LG8, and LG3. QTL-Plant hight, QTL-Fresh bast weight, QTL-Dry bast weight and QTL-fiber weight were related to fiber yield, while QTL-fiber strength and QTL-fiber count were related to fiber quality. This is the first study of its kind to map QTL of fiber yield and fiber quality, which will facilitate further understanding of the molecular genetic basis of these traits. However, there are limitations regarding the utilization of this map because several large gaps remain in some linkage groups. Therefore, additional markers need to be developed to further narrow these regions.

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits.

SummaryRamie is an important fibre‐producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield‐related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin‐signalling‐repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield‐related genetic loci and large‐scale genomic variation represent valuable resources for genomics‐assisted breeding of this crop.

Genome-wide association analysis of fiber fineness and yield in ramie (Boehmeria nivea) using SLAF-seq

Ramie (Boehmeria nivea L. Gaudich) is a major natural fiber crop cultivated in East Asia. The improvement of its fiber yield and fineness are important breeding goals. Fiber yield is a complex quantitative trait comprising ramet number, stem diameter, plant height, skin thickness, and fiber percentage. The fiber fineness is a crucial trait for ramie fiber quality. However, there are few association studies for fiber yield traits and fiber fineness on ramie, and lack high-density SNP maps in natural ramie population. Here, a panel of 112 core ramie germplasms were genotyped by 215,376 consistent single-nucleotide polymorphisms (SNPs) from specific-locus amplified-fragment sequencing (SLAF-seq), and used for genome-wide association study of fiber fineness and yield. Subsequently, the genetic diversity, linkage disequilibrium (LD), and population structure was conducted based on 215,376 SNPs. Population cluster analysis disclosed five subpopulations. Neighbor-joining (NJ) analysis revealed three major clusters. No obvious relationships were identified between them and their geographic origins. The genome-wide LD decayed to r2 = 0.1 was ~ 11.75 kbp in physical distance. One, seven, one, seven, and twenty-seven significant SNP marker associations were detected for fiber fineness (third season), stem diameter (third season), stem skin thickness (third season), fiber percentage (second season), and fiber percentage (third season), respectively. Two promising candidate genes, whole_GLEAN_10029622 and whole_GLEAN_10029638 resided in the significant trait-SNP association for fiber fineness (third season), which annotated as a cotton fiber-expressed protein and an Arabidopsis thaliana homebox protein ATH1, respectively and validated by qPCR. The identified loci or genes for fiber fineness and yield may provide the basis for future research on fiber fineness and yield and marker-assisted selection breeding for ramie.

SSR markers associated with fiber yield traits in ramie (Boehmeria nivea L. Gaudich)

Marker-assisted selection (MAS) can effectively promote fiber yield improvement for ramie. However, so far, the lack of molecular markers associated with fiber yield traits impede the application of MAS in ramie breeding. The objectives of this study were to identify simple sequence repeat (SSR) loci associated with fiber yield traits in ramie and to infer population structure and evolutionary genetic relationships. Genetic diversity, population structure, and association mapping analyses were conducted using 107 ramie accessions and 95 pairs of SSR markers. The results indicate that the average number of alleles per locus was 2.64 and that Shannon diversity index values ranged from 0.3797 to 1.4298. The 107 accessions were divided into two subpopulations with extensive genetic variation, indicating that the natural population was representative and could be used for further association analysis of quantitative traits. Association analysis detected a total of 16 stable molecular markers related to yield traits in ramie, including six for plant height, two for ramet number, five for stem diameter, three for skin thickness, and three for fiber percentage. Of these, the SSR marker RAM290 was associated with stem diameter in three environments and can explain 8.32%–23.42% of the phenotypic variation, indicating its potential utility in molecular breeding. These findings will be useful in the genetic improvement of ramie yield traits through marker-assisted selection.

High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing

BackgroundGenetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups.ResultsAn F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance.ConclusionsTo our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.

Identification of Chromosome Segment Substitution Lines of Gossypium barbadense Introgressed in G. hirsutum and Quantitative Trait Locus Mapping for Fiber Quality and Yield Traits.

Chromosome segment substitution lines MBI9804, MBI9855, MBI9752, and MBI9134, which were obtained by advanced backcrossing and continuously inbreeding from an interspecific cross between CCRI36, a cultivar of upland cotton (Gossypium hirsutum) as the recurrent parent, and Hai1, a cultivar of sea island cotton (G. barbadense) as the donor parent, were used to construct a multiple parent population of (MBI9804×MBI9855)×(MBI9752×MBI9134). The segregating generations of double-crossed F1 and F2 and F2:3 were used to map the quantitative trait locus (QTL) for fiber quality and yield-related traits. The recovery rate of the recurrent parent CCRI36 in the four parental lines was from 94.3%–96.9%. Each of the parental lines harbored 12–20 introgressed segments from Hai1across 21 chromosomes. The number of introgressed segments ranged from 1 to 27 for the individuals in the three generations, mostly from 9 to 18, which represented a genetic length of between 126 cM and 246 cM. A total of 24 QTLs controlling fiber quality and 11 QTLs controlling yield traits were detected using the three segregating generations. These QTLs were distributed across 11 chromosomes and could collectively explain 1.78%–20.27% of the observed phenotypic variations. Sixteen QTLs were consistently detected in two or more generations, four of them were for fiber yield traits and 12 were for fiber quality traits. One introgressed segment could significantly reduce both lint percentage and fiber micronaire. This study provides useful information for gene cloning and marker-assisted breeding for excellent fiber quality.

Evaluation of sunnhemp (Crotalaria juncea) genotypes for high fibre yield

Four genetically different genotypes of sunnhemp (Crotalaria juncea L.) were evaluated for fibre yield and its yield component traits for three years 2008-2009 to 2010-2011 at Sunnhemp Research Station, Pratapgarh, Uttar Pradesh. Significant differences among experimental genotypes were recorded for fibre yield and its attributes. High fibre yield/ha was recorded for SUIN-029 (9.06 q/ha) followed by SUIN-80 (8.94 q/ha). The highest green biomassyield (337.30 q/ha) and stick yield (52.41 q/ha) were recorded for SUIN-029. The analysis of the data for all years revealed superiority of genotype SUIN-029 for most of the fibre yield traits. This genotype can be used as donor for future breeding programme.

QTL identification for molecular breeding of fibre yield and fibre quality traits in jute

In jute (Corchorus olitorius), quantitative trait loci (QTL) analysis was conducted to study the genetics of eight fibre yield traits and two fibre quality traits. For this purpose, we used a mapping population consisting of 120 recombinant inbred lines (RILs) and also used a linkage map consisting of 36 SSR markers that was developed by us earlier (Das et al. 2011). The RIL population was derived from the cross JRO 524 (coarse fibre) × PPO4 (fine fibre) following single seed descent. Using single-locus analysis involving composite interval mapping, a total of 21 QTLs were identified for eight fibre yield traits whereas for fibre quality (fibre fineness), only one QTL was detected. The QTL for fibre fineness explained 8.31–10.56% of the phenotypic variation and was detected in two out of three environments. Using two-locus analysis involving QTLNetwork, as many as 11 M-QTLs were identified for seven fibre yield traits (excluding top diameter) and one M-QTL was identified for fibre fineness which accounted for 4.57% of the phenotypic variation. For six fibre yield traits, we detected 16 E-QTLs involved in nine QQ epistatic interactions. For fibre fineness, four E-QTLs involved in two QQ epistatic interactions and for fibre strength, six E-QTLs involved in three QQ epistatic interactions were identified. Eight out of the 11 M-QTLs observed for the fibre yield traits were also involved in QE interactions; for fibre fineness and fibre strength, no QE interactions were observed.