Distinguishing upland and lowland rice ecotypes by selective SSRs and their applications in molecular-assisted selection of rice drought resistance

Abstract

Upland and lowland rices (Oryza sativa) are the two most important rice ecotypes adapted to agricultural ecosystems of contrasting soil water conditions. Consequently, they have distinguished genetic features associated with drought resistance. As they are essential germplasm resources for breeding water-saving and drought-resistant rice, effective methods for discriminating rice ecotypes and evaluating their drought resistances are required. Five and three selective SSR loci respectively for japonica and indica, located in the drought-responding expression sequence tags (EST), were involved in this study. The discriminating index was calculated from the allele frequencies of these EST-SSRs between the two ecotypes. The discriminating index of upland rice was significantly higher than that of lowland rice. Moreover, the discriminating index had distinct distribution patterns between upland and lowland ecotypes. There were ecotype-like gradients of the discriminating index in which most landraces of the corresponding ecotype were located. Using the ecotype-like gradients, we can accurately distinguish upland and lowland rice with a discriminating power of 0.89 in japonica and 0.82 in indica. Noticeably, the discriminating index was significantly correlated with rice drought resistance; therefore, it greatly facilitates the process of drought-resistance screens. As these drought-resistance-associated EST-SSRs were divergently selected among upland and lowland rice, the discriminating index can be well applied in the practices of germplasm collection and breeding. The findings bridge the knowledge gaps between population genetics and breeding practice. Once more informative loci have been involved, the powers for ecotype discrimination and drought-resistance prediction will be improved.

Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia

“…SMRT sequencing technology has been successfully applied to full-length transcriptome sequencing studies in animals, plants and insects 26 – 28 . Furthermore, full-length transcriptome sequences obtained using SMRT sequencing contain numerous EST SSRs 29 , 30 , which can be used for genetic analyses of the sequenced species and their related species, as well as for studies of conservation biology and molecular assisted breeding 23 , 31 , 32 . To the best of our knowledge, no full-length transcriptome sequence of P. catalpifolia has been reported.…”

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

“…Among morphological traits for drought resistance, such as root characteristics [ 45 ], leaf rolling [ 46 ] and ratio of shoot and root [ 47 ], root length and root thickness have been positively related to field drought resistance [ 48 , 49 ], implying that robust roots can be used to distinguish upland and lowland rice. Further genetic differentiation between upland and lowland rice was explored by simple sequence repeats (SSRs) located in expressed sequence tags (ESTs) isolated from rice in response to drought treatment [ 44 , 50 ]. These previous studies suggested that there was considerable morphologic and genetic differentiation between upland and lowland rice.…”

Natural variation in the promoter of rice calcineurin B‐like protein10 (OsCBL10) affects flooding tolerance during seed germination among rice subspecies

“…With prolonged growth in these particular habitats, rice cultivars form habitat-specific characteristics with complex internal and external perceptions and response mechanisms from natural selection (Uddin et al, 2016). Once they are exposed to an environment different from their original habitats, alternative strategies need to be employed to counteract the negative effects triggered by abiotic stresses to ensure normal plant development (Colmer, 2002;Xia et al, 2015). Thus, an increasing number of comparative studies have been performed among different rice cultivars to unravel underlying adaptive mechanisms in the last decade (Xia et al, 2015).…”