Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones

Abstract

Background White Guinea yam (Dioscorea rotundata) is primarily a dioecious species with distinct male and female plants. Its breeding is constrained by sexual reproduction abnormalities, resulting in low success rates in cross-pollination. An accurate method for early detection of this plant’s sex and compatible fertile parents at the seedling stage would improve levels of cross-pollination success in breeding. We used the genome-wide association studies (GWAS) to dissect the molecular basis of plant sex and cross-compatibility-related traits in a panel of 112 parental clones used in D. rotundata crossing blocks from 2010 to 2020. Results Population structure and phylogeny analyses using 8326 single nucleotide polymorphism (SNP) markers grouped the 112 white yam clones into three subpopulations. Using Multi-locus random-SNP-effect Mixed Linear Model, we identified three, one, and three SNP markers that were significantly associated with the average crossability rate (ACR), the percentage of high crossability (PHC), and the plant sex, respectively. In addition, five genes considered to be directly linked to sexual reproduction or regulating the balance of sex hormones were annotated from chromosomal regions controlling the assessed traits. This study confirmed the female heterogametic sex determination (ZZ/ZW) system proposed for D. rotundata. Conclusions This study provides valuable insights on the genomic control of sex identity and cross-pollination success in D. rotundata. It, therefore, opens an avenue for developing molecular markers for predicting plant sex and cross-pollination success at the early growth stage before field sex expression in this crop.

Optimum time for hand pollination in yam (Dioscorea spp.)

“…Yam breeding is challenged by sexual reproduction abnormalities (sparse, irregular, and asynchronous flowering, cross compatibility barriers and low fertility) because of the domestication process that favored vegetative propagation at the expense of botanical seeds [ 3 , 15 ]. The International Institute of Tropical Agriculture (IITA) has devised a series of studies to control those reproduction abnormalities.…”

“…Data collected on the fruit and seed sets were further used to calculate the pollination success rate, the seed setting rate (SSR), the seed production efficiency (SPE), and the seed viability (SV) as in Mondo et al [ 4 , 27 ] and Asfaw et al [ 15 ]. The pollination success rate was calculated as follows: …”

“…alata and D . rotundata , are dioecious with male and female flowers on separate individuals [ 3 , 4 , 13 – 15 ]. The gene flow between and among these species to meet breeding objectives depends, therefore, on cross-pollination success.…”

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

“…Such analysis has been employed in many crops (including yam) to explore the alleles for enhancing agronomic, flower sex and biotic stress tolerance. 14,23,[52][53][54][55]…”

“…The prediction for the lowest index value refers to the closeness to the ideal genotype and thus indicates the desired quality for BY/PY food product. Such analysis has been employed in many crops (including yam) to explore the alleles for enhancing agronomic, flower sex and biotic stress tolerance 14,23,52‐55 …”