Latitudinal Distribution and Differentiation of Rice Germplasm: Its Implications in Breeding

Abstract

To determine genetic differentiation of rice (Oryza sativa L.) across a latitudinal gradient, a total of 386 rice varieties, five African rice varieties, and 52 wild rice accessions mainly from a wide range of Asia were analyzed using insertion and deletion (InDel) molecular markers. Principal component analysis divided rice into two distinct groups, although African rice and wild rice did not show such grouping. Results indicated significant indica–japonica differentiation of rice adapted to a wide range of environments, contrasting with African rice and wild rice. Analysis of the geographic distribution indicated a clear pattern for different types of rice, in which indica varieties were found across a wide range of latitudes from ∼2° S to 40° N and japonica mostly limited to latitudes greater than 15° N. Most intermediate types were distributed in regions at latitudes lower than 27° N. Correlation between rice types and temperature along the latitude gradients suggested that indica varieties are less sensitive to temperature along the latitude ranges but japonica varieties are highly sensitive to temperature. The distribution and differentiation of various types of rice across the large latitudinal range is most likely the consequence of their adaptation to ecological and environmental factors, especially temperature. This, together with the accurate determination of indica and japonica types has important implications for hybrid rice breeding through selecting properly differentiated parents.

Genetic Differentiation of Asian Weedy Rice Revealed with InDel Markers

“…We found that only seven of the 142 Asian weedy rice entries belong to an intermediate type with a low level of differentiation, whereas the vast majority of the entries did not fall into the consecutive F i range between 0.25 and 0.75. Furthermore, there is a high frequency of gene flow among japonica rice, indica rice, and common wild rice (Song et al, 2004;Xiong et al, 2011;Xu et al, 2012). This finding is in good agreement with the findings of previous studies on the genetic differentiation of cultivated rice, suggesting that the indica rice is mainly distributed in the southeast of Asia and the south of China and japonica rice is mainly distributed in Japan, Korea, and northeast China, and thus there is a significant differentiation of indica rice and japonica rice (Liu et al, 2012;Lu et al, 2009;Xu et al, 2009;Zhang et al, 2005).…”

“…However, there are currently four major hypotheses regarding the occurrence of this weed: (i) some populations gradually evolved from common wild rice; (ii) some populations resulted from natural crossing of common wild rice and cultivated rice; (iii) some populations are trait segregating progenies of the hybrid of phylogeographically distant indica and japonica rice; and (iv) some populations are examples of atavism in which some traits of the ancestral common wild rice were suddenly recovered (Londo and Schaal, 2007;Wang et al, 2005;Wu et al, 2007). Currently, a number of research institutions in China and other countries are carrying out certain levels of collection, control, and differentiation studies on weedy rice, mainly focusing on origin theory identification and the discovery of the relationships among weedy rice, common wild rice, and cultivated rice (Xia et al, 2011;Xiong et al, 2011Xiong et al, , 2012Xu et al, 2012).…”

“…Recently, on the basis of the insertion and deletion (InDel) fragments in the DNA sequences of the entire genomes of the typical indica rice variety 93-11 and japonica rice Nipponbare (Shen et al, 2004), Lu et al (2009) developed an "InDel molecular index" for the identification of indica or japonica rice varieties. It also can be used to differentiate weedy rice, a widespread, notorious weed that coexists with rice in paddy fields worldwide (Lu et al, 2009;Xiong et al, 2011Xiong et al, , 2012. It also can be used to differentiate weedy rice, a widespread, notorious weed that coexists with rice in paddy fields worldwide (Lu et al, 2009;Xiong et al, 2011Xiong et al, , 2012.…”

“…This method has made the study of indica-japonica differentiation in a large set of rice germplasm feasible without the influence of the experimental environments where the rice is grown for study. It also can be used to differentiate weedy rice, a widespread, notorious weed that coexists with rice in paddy fields worldwide (Lu et al, 2009;Xiong et al, 2011Xiong et al, , 2012. In addition, it is possible for the first time to characterize indica-japonica differentiation quantitatively using the InDel frequency (ranging between 0 and 1) of indica-or japonica-specific alleles from across the rice genome because the I-or J-allelic frequencies can be calculated (for details see Lu et al, 2009;Xiong et al, 2010).…”

Overcoming inter-subspecific hybrid sterility in rice by developing indica-compatible japonica lines

“…Currently used rice varieties with a close genetic relationship have limited heterosis, leading to a yield plateau for indica hybrid rice production7. Strong heterosis exists in the inter-subspecific hybrids and the exploitation of this heterosis has long been considered as a promising way to further increase rice yield potential458. However, the major obstacle of utilizing the heterosis between the subspecies is the strong hybrid sterility39101112.…”