Gao Ming, Hua Tien, Niu Genhua, Masabni Joe, Dewalt Willie
Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States.
AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States.
Front Plant Sci. 2024 May 28;15:1398081. doi: 10.3389/fpls.2024.1398081. eCollection 2024.
Two interrelated aspects of the sweetpotato genome, its polyploid origin and inheritance type, remain uncertain. We recently proposed a segmental allohexaploid sweetpotato and thus sought to clarify its inheritance type by direct analyses of homoeolog segregations at selected single-copy loci. For such analyses, we developed a digital quantitative PCR genotyping method using one nondiscriminatory and three discriminatory probes for each selected locus to discriminate and quantify three homoeolog-differentiating variation types (homoeolog-types) in genomic DNA samples for genotype fitting and constructed a F2 population for segregation analyses. We confirmed inter-subgenomic distinctions of three identified homoeolog-types at each of five selected loci by their interspecific differentiations among 14 species in Ipomoea section batatas and genotyped the loci in 549 F2 lines, selected F1 progenies, and their founding parents. Segregation and genotype analyses revealed a locus-dependent mixed inheritance (disomic, polysomic, and intermediate types) of the homoeolog-types at 4 loci in the F2 population, displaying estimated disomic-inheritance frequencies of 0, 2.72%, 14.52%, and 36.92%, and probably in the F1 population too. There were also low-frequency non-hexaploid F1 and F2 genotypes that were probably derived from double-reduction recombination or partially unreduced gametes, and F2 genotypes of apparent aneuploids/dysploids with neopolyploid-like frequencies. Additional analyses of homoeolog-type genotypes at the 5 loci in 46 lines from various regions revealed locus-dependent selection biases, favoring genotypes having more of one homoeolog-type, i.e. more of di- or homogenized homoeolog-type composition, and one-direction ploidy trending among apparent aneuploids/dysploids. These inheritance features pointed to an evolving segmental allohexaploid sweetpotato impacted by selection biases.
甘薯基因组的两个相互关联的方面，即其多倍体起源和遗传类型，仍不明确。我们最近提出甘薯是节段异源六倍体，因此试图通过直接分析选定单拷贝位点的同源基因分离情况来阐明其遗传类型。对于此类分析，我们开发了一种数字定量PCR基因分型方法，针对每个选定位点使用一个非歧视性探针和三个歧视性探针，以区分和量化基因组DNA样本中的三种同源基因差异变异类型（同源基因类型），用于基因型拟合，并构建了一个F2群体用于分离分析。我们通过在甘薯组14个物种间的种间分化，确认了在五个选定位点上每个位点的三种已鉴定同源基因类型的亚基因组差异，并对549个F2品系、选定的F1后代及其亲本进行了基因分型。分离和基因型分析显示，F2群体中4个位点的同源基因类型存在位点依赖性混合遗传（二体、多体和中间类型），估计二体遗传频率分别为0%、2.72%、14.52%和36.92%，F1群体可能也是如此。也存在低频非六倍体F1和F2基因型，可能源自双减数重组或部分未减数配子，以及具有新多倍体样频率的明显非整倍体/发育异常的F2基因型。对来自不同地区的46个品系中5个位点的同源基因类型基因型的进一步分析揭示了位点依赖性选择偏差，倾向于具有更多一种同源基因类型的基因型，即更多二体或同质化同源基因类型组成，以及明显非整倍体/发育异常个体中的单向倍性趋势。这些遗传特征表明，甘薯是一种受选择偏差影响而不断进化的节段异源六倍体。
