Genetic analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs

Abstract

Knowledge of natural diversity and population structures of wild species, which might be related to cultivated species, is fundamental for conservation and breeding purposes. In this study, a genetic characterization of a large population of Oryza glumaepatula, occurring in a 10 km(2) area located at Tamengo Basin (Paraguay River, Brazil), was performed using SSR markers. This population is annually dragged from the river to permit navigation; one goal of this study was to examine the impact of this removal on genetic variability. From 18 polymorphic SSR markers, a total of 190 alleles were detected in a sample of 126 individuals, with an average of 10.3 alleles/locus, and a H(e) of 0.67. The five QTL-related markers showed an average H(e) value of 0.56, while the remaining 13 markers detected an average estimate of 0.70. An apparent outcrossing rate of 30%, a high proportion of alleles at low frequencies (56%), and the presence of exclusive alleles (9.5%) were found, with strong evidence of the establishment of individuals from different populations upstream in the Paraguay River. For conservation purposes, the river drag has no effect on the population. However, periodical seed collection from the Corumbá population can preserve part of the genetic variability present in upstream populations reducing the need for upriver collecting expeditions.

Genetic diversity inOryza glumaepatulawild rice populations in Costa Rica and possible gene flow fromO. sativa

“…This population may be large enough to preserve a significant proportion of the original genetic diversity. Similar results were found for other large and similarly interconnected populations in Brazil ( Buso, Rangel & Ferreira, 1998 ; Vaz et al, 2009 ).…”

“…Migration between sub-populations may occur at the beginning of the rainy season (May), when seeds and culms are likely carried along the river. Vaz et al (2009) reached similar conclusions and did not find evidence of structure among samples collected along the same river separated by ∼10 km. Studies that found structure ( Akimoto, Shimamoto & Morishima, 1998 ; Buso, Rangel & Ferreira, 1998 ; Brondani et al, 2005 ; Karasawa et al, 2007b ) consistently analyzed populations separated by large distances (>100 km), and in most cases in different unconnected river systems.…”

EST-SSR Based Genetic Diversity and Population Structure among Korean Landraces of Foxtail Millet (Setaria italica L.)

“…The highly polymorphic EST-SSR markers resulted out 121 alleles with an average of 5.5 alleles per locus, which was comparable to other studies such as 4.91 in broomcorn millet, 4.79 in sorghum, 3.93 in rice, 8.2 in maize, 6.16 and 2.4 in foxtail millet, and 7.6 in sorghum (Cho et al, 2000;Agrama et al, 2007;Hu et al, 2009;Shehzad et al, 2009;Jia et al, 2009;Lin et al, 2012). The HE mean value in the present study (0.594) was higher than that reported in proso millet (0.37), while less than that reported in rice (0.67) (De campos et al, 2008;Cho et al, 2010). Similarly, the Ho average value (0.034) was slightly closer to Indian foxtail millet (0.045) (Gupta et al, 2012).…”

Yield QTL analysis of Oryza sativa x O. glumaepatula introgression lines

“…It grows along riverbeds and margins or as isolated populations, in lowland conditions, far from the rivers (known as marshy valleys), in which case it has a behavior typical of weeds or colonizing plants (Brondani et al, 2001). Oryza glumaepatula has been extensively studied (Vaz et al, 2009), due to its close genetic relationship to cultivated rice and, especially, because it has the potential to successfully transfer favorable yield-related alleles, promoting positive increases in cultivated rice architecture and grain yield (Brondani et al, 2002;Rangel et al, 2005). Oryza glumaepatula has been used as allele donor to elite lines (O. sativa) from the Brazilian rice breeding program since 1996 (Brondani et al, 2001).…”