Identification and validation of QTLs for tuber quality related traits in greater yam (Dioscorea alata L.)

Genome-wide association analysis and transgenic characterization for amylose content regulating gene in tuber of Dioscorea zingiberensis

BACKGROUND

Amylose, a prebiotic found in yams is known to be beneficial for the gut microflora and is particularly advantageous for diabetic patients' diet. However, the genetic machinery underlying amylose production remains elusive. A comprehensive characterization of the genetic basis of amylose content in yam tubers is a prerequisite for accelerating the genetic engineering of yams with respect to amylose content variation.

RESULTS

To uncover the genetic variants underlying variation in amylose content, we evaluated amylose content in freshly harvested tubers from 150 accessions of Dioscorea zingibensis. With 30,000 high-quality single nucleotide polymorphisms (SNP), we performed a genome-wide association analysis (GWAS). The population structure analysis classified the D. zingiberensis accessions into three groups. A total of 115 significant loci were detected on four chromosomes. Of these, 112 significant SNPs (log10(p) = 5, q-value < 0.004) were clustered in a narrow window on the chromosome 6 (chr6). The peak SNP at the position 75,609,202 on chr6 could explain 63.15% of amylose variation in the population and fell into the first exon of the ADP-glucose pyrophosphorylase (AGPase) small subunit gene, causing a non-synonymous modification of the resulting protein sequence. Allele segregation analysis showed that accessions with the rare G allele had a higher amylose content than those harboring the common A allele. However, AGPase, a key enzyme precursor of amylose biosynthesis, was not expressed differentially between accessions with A and G alleles. Overexpression of the two variants of AGPase in Arabidopsis thaliana resulted in a significantly higher amylose content in lines transformed with the AGPase-G allele.

CONCLUSIONS

Overall, this study showed that a major genetic variant in AGPase probably enhances the enzyme activity leading to high amylose content in D. zingiberensis tuber. The results provide valuable insights for the development of amylose-enriched genotypes.

Quantitative trait loci and candidate genes for physico-chemical traits related to tuber quality in greater yam (Dioscorea alata L.)

BACKGROUND

Starch, dry matter content (DMC), proteins, and sugars are among the major influences on yam tuber quality. Genetic improvement programs need simple, rapid, and low-cost tools to screen large populations. The objectives of this work were, using a quantitative trait loci mapping approach (QTL) on two diploid full-sib segregating populations, (i) to acquire knowledge about the genetic control of these traits; (ii) to identify markers linked to the genomic regions controlling each trait, which are useful for marker-assisted selection (MAS); (iii) to validate the QTLs on a diversity panel; and (iv) to identify candidate genes from the validated QTLs.

RESULTS

Heritability for all traits was moderately high to high. Significant correlations were observed between traits. A total of 25 QTLs were identified, including six for DMC, six for sugars, six for proteins, and seven for starch. The phenotypic variance explained by individual QTLs ranged from 14.3% to 28.6%. The majority of QTLs were validated on a diversity panel, showing that they are not specific to the genetic background of the progenitors. The approximate physical location of validated QTLs allowed the identification of candidate genes for all studied traits. Those detected for starch content were mainly enzymes involved in starch and sucrose metabolism, whereas those detected for sugars were mainly involved in respiration and glycolysis.

CONCLUSION

The validated QTLs will be useful for breeding programs using MAS to improve the quality of yam tubers. The putative genes should be useful in providing a better understanding of the physiological and molecular basis of these important tuber quality traits. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genome-wide dissection of the genetic factors underlying food quality in boiled and pounded white Guinea yam

BACKGROUND

Food quality traits related to the genetics of yam influence the acceptability for its consumption. This study aimed at identifying genetic factors underlying sensory and textural quality attributes of boiled and pounded yam, the two dominant food products from white Guinea yam.

RESULTS

A genome-wide association study (GWAS) of a panel of 184 genotypes derived from five multi-parent crosses population was conducted. The panel was phenotyped for the qualities of boiled and pounded yam using sensory quality and instrument-based textural profile assays. The genotypes displayed significant variation for most of the attributes. Population differentiation and structure analysis using principal component analysis (PCA) and population structure-based Bayesian information criteria revealed the presence of four well-defined clusters. The GWAS results from a multi-random mixed linear model with kinship and PCA used as covariate identified 13 single-nucleotide polymorphic (SNP) markers significantly associated with the boiled and pounded yam food qualities. The associated SNP markers explained 7.51-13.04% of the total phenotypic variance with a limit of detection exceeding 4.

CONCLUSION

Regions on chromosomes 7 and 15 were found to be associated with boiled and pounded yam quality attributes from sensory and instrument-based assays. Gene annotation analysis for the regions of associated SNPs revealed co-localization of several known putative genes involved in glucose export, hydrolysis and glycerol metabolism. Our study is one of the first reports of genetic factors underlying the boiled and pounded yam food quality to pave the way for marker-assisted selection in white Guinea yam. © 2023 Society of Chemical Industry.

Genome-wide association studies reveal novel loci controlling tuber flesh color and oxidative browning in Dioscorea alata

BACKGROUND

Consumers' preferences for food crops are guided by quality attributes. This study aimed at deciphering the genetic basis of quality traits, especially tuber flesh color (FC) and oxidative browning (OB) in Dioscorea alata, based on the genome-wide association studies (GWAS) approach. The D. alata panel was planted at two locations in Guadeloupe. At harvest, the FC was scored visually as white, cream, or purple on longitudinally sliced mature tubers. The OB was scored visually as the presence or absence of browning after 15 min of exposure of the sliced samples to ambient air.

RESULTS

Phenotypic characterization for FC and OB of a diverse panel of D. alata genotypes highlighted significant variation within the panel and across two locations. The genotypes within the panel displayed a weak structure and could be classified into three subpopulations. GWAS identified 14 and 4 significant associations for tuber FC and OB, respectively, with phenotypic variance, explained values ranging from 7.18% to 18.04%. Allele segregation analysis at the significantly associated loci highlighted the favorable alleles for the desired traits, i.e., white FC and no OB. A total of 24 putative candidate genes were identified around the significant signals. A comparative analysis with previously reported quantitative trait loci indicated that numerous genomic regions control these traits in D. alata.

CONCLUSION

Our study provides important insights into the genetic control of tuber FC and OB in D. alata. The major and stable loci can be further utilized to improve selection in breeding programs for developing new cultivars with enhanced tuber quality. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata

BACKGROUND

Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam.

METHODS AND RESULTS

Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, β-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data.

CONCLUSIONS

The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.

Variability and genetic merits of white Guinea yam landraces in Nigeria

INTRODUCTION

Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as a potential donor of important traits such as resilience to stresses as well as food quality attributes that may be useful in modern yam breeding. This study assessed the pattern of genetic variability, quantitative trait loci (QTLs), alleles, and genetic merits of landraces, which could be exploited in breeding for more sustainable yam production in Africa.

METHODS

A total of 86 white Guinea yam landraces representing the popular landraces in Nigeria alongside 16 elite clones were used for this study. The yam landraces were genotyped using 4,819 DArTseq SNP markers and profiled using key productivity and food quality traits.

RESULTS AND DISCUSSION

Genetic population structure through admixture and hierarchical clustering methods revealed the presence of three major genetic groups. Genome-wide association scan identified thirteen SNP markers associated with five key traits, suggesting that landraces constitute a source of valuable genes for productivity and food quality traits. Further dissection of their genetic merits in yam breeding using the Genomic Prediction of Cross Performance (GPCP) allowed identifying several landraces with high crossing merit for multiple traits. Thirteen landraces were identified as potential genitors to develop segregating progenies to improve multiple traits simultaneously for desired gains in yam breeding. Results of this study provide valuable insights into the patterns and the merits of local genetic diversity which can be utilized for identifying desirable genes and alleles of interest in yam breeding for Africa.