Genome-Wide SNPs Provide Insights on the Cryptic Genetic Structure and Signatures of Climate Adaption in Amorphophallus albus Germplasms

Abstract

Domesticated species represent unique systems in which the evolutionary genomic consequences of intensive selective breeding and adaptation can be thoroughly investigated. Amorphophallus albus occurs naturally and is in cultivation throughout the downstream region of the Jinshajiang River in Southwest China. This species is characterised by high konjac glucomannan content, and has been cultivated in China for nearly 2,000 years. To study genetic differentiation and local adaption of A. albus, we sampled 13 distinct local cultivated populations of this species. Restriction site-associated DNA sequencing was conducted with 87 samples, resulting in 24,225 SNPs. The population structure analyses suggest two main genetic groups: one in the relatively upstream region, and one downstream. We found evidence of additional sub-structure within the upstream group, demonstrating the statistical power of genomic SNPs in discovering subtle genetic structure. The environmental and geographic factors were all identified as significant in shaping the genetic differentiation of this species. Notably, the proportion of environmental factors was larger than geographic factors in influencing the population genetic patterns of A. albus. We also discovered loci that were associated with local adaptation. These findings will help us understand the genetic differentiation of this newly domesticated species, thereby informing future breeding programs of A. albus.

Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China

“…These results suggested a pattern of generally low population genetic diversity and high genetic differentiation of A. yunnanensis . Similar patterns of genetic variation have also been observed in populations of other Amorphophallus species, such as A. konjac and A. albus (Gao et al., 2018 , 2021 ). Amorphophallus are protogynous plant species, and the flowers send forth a strong odor to attract rove beetles as pollinators once pistils are mature (Tang et al., 2020 ).…”

“…However, species in the Amorphophallus genus have large genomes (3.70–15.48 Gb), so reduced‐representation library sequencing is a more effective technology for such taxa than whole‐genome sequencing (Gargiulo et al., 2021 ; Tao et al., 2021 ). Restriction‐site‐associated DNA sequencing (RAD‐seq) has been employed in population genetic studies of several Amorphophallu s species, such as A. paeoniifolius and A. albus (Gao et al., 2017 , 2021 ). While previous research focuses primarily on the genomic variation of cultivated resources of Amorphophallu s, the evolutionary history of wild populations has not been investigated.…”

Population and Landscape Genetics Provide Insights Into Species Conservation of Two Evergreen Oaks in Qinghai–Tibet Plateau and Adjacent Regions

“…By contrast, we detected significant IBE patterns in Q. aqu -East and Q. spi -West lineage ( Table 4 and Supplementary Figure 5 , Supplementary Tables 5 , 6 ), where the extreme environmental conditions on the plateau might be regarded as a significant climatic barrier, rather than a geographic barrier. It also suggests that geographic isolation may cause interspecific and intraspecific differentiation; adaptation to local climate and environmental factors reinforces this differentiation and gradually forms this significant IBE pattern ( Gao et al, 2021 ). Accordingly, GDM and RDA both suggesting temperature annual range (bio07) and precipitation during June (prec06) were the most significant environmental factor driving genetic variation in Q. aqu -East and Q. spi -West lineage ( Figure 6 , Table 5 and Supplementary Figure 4 , Supplementary Table 6 ), respectively.…”