Polymorphism analysis of the chloroplast and mitochondrial genomes in soybean

Abstract

Background Soybean is an important protein- and oil-rich crop throughout the world. Much attention has been paid to its nuclear genome, which is bi-parentally inherited and associated with many important agronomical traits. However, less is known about the genomes of the semi-autonomous and essential organelles, chloroplasts and mitochondria, of soybean. Results Here, through analyzing the polymorphisms of these organelles in 2580 soybean accessions including 107 wild soybeans, we found that the chloroplast genome is more variable than the mitochondrial genome in terms of variant density. Consistent with this, more haplotypes were found in the chloroplast genome (44 haplotypes) than the mitochondrial genome (30 haplotypes). These haplotypes were distributed extremely unevenly with the top two haplotypes (CT1 and CT2 for chloroplasts, MT1 and MT2 for mitochondria) accounting for nearly 70 and 18% of cultivated soybean accessions. Wild soybeans also exhibited more diversity in organelle genomes, harboring 32 chloroplast haplotypes and 19 mitochondrial haplotypes. However, only a small percentage of cultivated soybeans shared cytoplasm with wild soybeans. In particular, the two most frequent types of cytoplasm (CT1/MT1, CT2/MT2) were missing in wild soybeans, indicating that wild soybean cytoplasm has been poorly exploited during breeding. Consistent with the hypothesis that soybean originated in China, we found that China harbors the highest cytoplasmic diversity in the world. The geographical distributions of CT1–CT3 and MT1–MT3 in Northeast China were not significantly different from those in Middle and South China. Two mitochondrial polymorphism sites, p.457333 (T > C) and p.457550 (G > A), were found to be heterozygous in most soybeans, and heterozygosity appeared to be associated with the domestication of cultivated soybeans from wild soybeans, the improvement of landraces to generate elite cultivated soybeans, and the geographic adaptation of soybean. Conclusions The haplotypes of thousands of soybean cultivars should be helpful in evaluating the impact of cytoplasm on soybean performance and in breeding cultivars with the desired cytoplasm. Mitochondrial heterozygosity might be related to soybean adaptation, and this hypothesis needs to be further investigated.

Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships

“…and mt genomes in the date palm was confirmed by the same analysis performed with another published date palm dataset [ 3 ]. A difference of the same magnitude, although of opposite direction, was observed in soybean [ 45 ] and Ginkgo [ 46 ] where Ts/Tv were 0.99 and 2.29 in mtDNA and 0.2 and 0.61 in cpDNA, respectively. It has already been reported that the rate of transversions can be slightly higher than that of transitions in the date palm mitochondrial genome [ 18 ].…”

Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data

“…This study analyzed the chloroplast genomes of 104 P. montana accessions, identifying 1118 SNPs and 556 indel variations with high intraspecies variability ( Table 1 ). P. montana chloroplast genome showed higher variability compared with other published plant species, such as Ginkgo biloba (135 SNPs, 71 accessions) [ 52 ], Brachypodium distachyon (298 SNPs, 53 accessions) [ 51 ], soybean (44 SNPs, 2580 accessions) [ 53 ], Coptis chinensis (111 SNPs, 227 accessions) [ 19 ], and Ulmus laevis (32 SNPs, 54 accessions). Mutation heterogeneity across different plant lineages or species has been previously examined.…”

Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding

“…Analysis of polymorphisms in 2580 soybean accessions, including 107 wild soybeans, revealed that the chloroplast genome is more variable than the mitochondrial genome in terms of variant density [ 70 ]. Cultivated soybeans harbored 44 chloroplast haplotypes and 30 mitochondrial haplotypes, with the two most frequent types accounting for nearly 70 and 18%, respectively [ 70 ]. Wild soybeans, on the other hand, had 32 chloroplast and 19 mitochondrial haplotypes.…”

“…However, only a small proportion of cultivated soybeans shared cytoplasm with wild soybeans. Two mitochondrial polymorphism sites were discovered to be heterozygous in most soybeans, suggesting a link between heterozygosity and domestication, improvement of landraces, geographic adaptation [ 70 ]. The haplotypes of many soybean cultivars could be beneficial for evaluating the impact of cytoplasm on performance, as well as for breeding cultivars with desired cytoplasm.…”

“…The haplotypes of many soybean cultivars could be beneficial for evaluating the impact of cytoplasm on performance, as well as for breeding cultivars with desired cytoplasm. It is possible that mitochondrial heterozygosity is associated with soybean adaptation, which requires further investigation [ 70 ].…”