Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the ...genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Despite the importance of and current demand for abaca (
Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy ...top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (
Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC
and BC
) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC
induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation.
The Musa textilis var. Abuab has high fiber quality (FQ) but is susceptible to abaca bunchy top virus (AbBTV); the Musa balbisiana var. Pacol has low FQ but is resistant against AbBTV. Their ...backcrosses (BC2 and BC3) possess both desirable traits. Analysis using RNA-seq showed that the regulatory divergence of Abuab and Pacol is largely explained by cis differences with 27.4% and 22.3% if we are to assess it using BC2 and BC3, respectively. Cis differences between the two genotypes are significantly reduced from BC2 to BC3 due to changes in genomic constitution. Trans, on the other hand, is robust to changes in allelic composition. All these are attributed to the loss of heterozygosity in BC3 relative to BC2. Further analysis showed that both backcrosses exhibited genome-wide preferential expression of Pacol- over Abuab-specific alleles, despite the wider genetic presence of the latter in the hybrids. The ratio of the two genotype-specific expressed transcripts and the ratio of their corresponding genetic make-up are significantly disproportionate, a phenomenon that we refer to here as “genome–transcriptome incongruence”. We also observed preferential expression switching in which several genes prefer the Abuab- (or Pacol-) specific allele in BC2 but switched to the Pacol- (or Abuab-) specific allele in the BC3 genome.
The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies ...(GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (
-value) ≥ 3.0. The
and
were consistently identified in all the four environments, ten QTLs
,
,
,
, and
were detected in two environments, while two major loci
and
were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as
for days to flowering,
for plant height, and
for grain length. Similarly,
and
genes were identified for BLB resistance and
, and
genes were identified for Blast resistance. A number of metal homeostasis genes
,
,
,
, and
were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.
The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high ...grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubled-haploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn
. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.
Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite ...Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz:
, and
, which can be used in rice genomics assisted breeding. A major QTL (
) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R
. In all, 26 QTL clusters were identified on different chromosomes.
epistatically interacted with
and
. Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of
was co-located with putative genes such as
,
, and
that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with
-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.
‘Sibujing' is an emerging crop species in the Philippines with recorded traditional use as condiment in localized areas in Mindanao. However, its taxonomic identity is confused as it has been ...attributed to various taxa of Allium. We characterized the morphological, phytochemical and molecular characteristics of a ‘sibujing' accession to establish the taxonomic belonging and correct species name of the crop and elucidate its baseline characteristics for its continued utilization. Through next‐generation sequencing, we assembled the quadripartite genome of a ‘sibujing' accession from Zamboanga del Norte. The generated chloroplast genome revealed 100% similarity to the earlier established 152 525‐bp‐long A. chinense G.Don. plastome from China. Morphological characteristics also support this identification as both bears leaves with hollow 3–5‐angled cross‐sections, scapes that are terete and solid, and distinctly toothed filament base. Saponins were also detected from its methanolic extract. Phylogenetic reconstruction based on the sequenced ITS region, a nuclear barcode, suggested that the species was closest to taxa belonging to Allium sect. Sacculiferum subg. Cepa, further supporting its potential identity with A. chinense. Using a separate accession from a different locality in the Philippines, these findings were validated as the chloroplast genome assembled, phytochemical and morphological characteristics recorded were similarly established as close to A. chinense. This is the first definitive record of an Allium species from sect. Sacculiferum in the Philippines.
The Philippines is one of the major rice-producing and rice-consuming countries of Asia. A large portion of its population depends on rice for their daily caloric intake and nutritional needs. The ...lack of dietary diversity among poor communities has led to nutritional consequences, particularly micronutrient deficiencies. Iron-deficiency anemia (IDA) and zinc deficiency (ZnD) are two serious nutritional problems that affect the health and economic sector of the country. Since rice dominates the Filipino diet by default, biofortification of rice will help improve the micronutrient status. The Philippine government has proactively initiated various programs and policies to address micronutrient deficiencies, particularly through fortification of basic food commodities. Biofortification, the fortification of rice with micronutrients through breeding, is considered the most sustainable and cost-effective strategy that can benefit large vulnerable populations. However, developing promising genotypes with micronutrient-enriched grains should be coupled with improving micronutrient bioavailability in the soil in order to optimize biofortification. This review documents the prevailing soil Zn-deficiency problems in the major rice production areas in the Philippines that may influence the Zn nutritional status of the population. The article also reports on the biofortification efforts that have resulted in the development of two biofortified varieties approved for commercial release in the Philippines. As nutritional security is increasingly recognized as a priority area, greater efforts are required to develop biofortified rice varieties that suit both farmers' and consumers' preferences, and that can address these critical needs for human health in a sustainable and cost-effective manner.
The three-leaved chaste tree (Vitex trifolia) is a medicinal and ornamental plant widely distributed from East Africa to the Pacific but has no complete chloroplast genome sequence. We assembled and ...characterized the V. trifolia accession from the germplasm collection of the Institute of Crop Science, University of the Philippines Los Baños. The complete plastome sequence is 154,444-bp long with 131 coding genes comprising 87 mRNA genes, 36 tRNA genes, and 8 rRNA genes. A phylogenetic analysis of the assembled genome, together with nine other Lamiaceae species, identified V. rotundifolia as its closest relative with available complete cpDNA sequence. The clustering also supports the genotypic similarity of the species belonging to trifolia group of the genus Vitex.
Pearl millet (
Pennisetum glaucum L. Leeke) is known to adapt to very dry conditions, however, the control of water loss and dehydration tolerance to drought is still not completely understood. ...Effects of water stress on root morphologies, osmotic relations, and stomatal conductance contributing to plant growth or turgor maintenance was investigated. Water stress was imposed by withholding water for 3 weeks at the seedling stage in a greenhouse. Irrigated treatments and two stress treatments were conducted in a tube culture experiment. One stress treatment was done by imposing water deficit, particularly in shallow areas of the soil (semi-drought), and the other was done by imposing widespread water deficit in the soil (drought).
The genetic diversities in the total root length (TRL) were significantly related to the relative growth ratio of the shoot (RGR) within 4–21 days after withholding water in both stress treatments. On the other hand, osmotic adjustment was also strongly correlated with RGR and leaf turgor potential (LTP) in both stress treatments, but the effects of TRL and OA in terms of contributing to the variance in RGR was comparatively low under drought conditions. These results demonstrated that OA and TRL were dependent on the degree of water deficit, and these traits were the most important factors regarding turgor maintenance and plant growth under drought conditions during the seedling stage.
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