Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

Abstract

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.) is one of the most important cereal crops in the world. There have been landmark achievements in rice improvement over the past 50 y, especially in the indica subspecies. A major breakthrough resulted from the independent development of a series of semidwarf varieties in China and by the International Rice Research Institute (IRRI) in the 1950s and 1960s, leading to the "green revolution" in rice. Since then, semidwarfness has been a basic characteristic for almost all modern varieties. Based on semidwarf varieties, improvement for other traits, such as abiotic stress resistance, broad-spectrum resistances to biotic stresses, and better grain quality, has also been achieved. Another major breakthrough stemmed from the exploitation of hybrid vigor in China (1), resulting in the largescale adoption of hybrid rice since the 1970s. Jointly, these breakthroughs have greatly increased rice productivity in the past several decades globally.Genomic studies in recent years have identified a large number of loci that were under selection during rice domestication (2). However, there has been very limited study to identify loci or genomic regions that have been under selection due to breeding. Next-generation sequencing technologies have enabled sequencing of a large number of rice accessions at relatively low cost, providing opportunities to inspect the genomic regions selected in the history of crop improvement. Meanwhile, genome-wide association studies (GWAS) have provided an effective approach to analyze the genetic architecture of complex traits and allow identification of candidate genes for further improvement of agronomically important traits (3,4).In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions, which revealed a large number of differentially selected regions associated with breeding efforts between two major subpopulations in indica. These selected regi...

Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields

“…The cross-population likelihood method (XP-CLR) was used to identify genetic selection signals. The XP-CLR data for these rice accessions showed that only OsNRT2.3 of the rice nitrate transporter genes was under selection pressure during evolution and was much stronger in Indica II compared with Indica I rice cultivars (29). Our expression data confirm the XP-CLR results, showing that there were two selection patterns in rice; that is, one group of rice cultivars had selection pressure on the expression ratio of OsNRT2.3b to OsNRT2.3a linking with N accumulation, whereas the other group lost this selection.…”

“…Our expression data confirm the XP-CLR results, showing that there were two selection patterns in rice; that is, one group of rice cultivars had selection pressure on the expression ratio of OsNRT2.3b to OsNRT2.3a linking with N accumulation, whereas the other group lost this selection. The division of rice cultivars in the responses of OsNRT2.3b and OsNRT2.3a expression to N supply may result from their different growth and cultivation conditions (29).…”

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

“…Higher nucleotide diversity observed among varieties in RP3 indicated an increase in diversity in the primary gene pool as result of recent chickpea breeding programs. Although, recent studies reported modern breeding processes had no significant change in diversity in several crop species535455. The number of selected haplotypes may serve as an indicator for evaluating the breeding potential of varieties to guide more efficient selection.…”

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

“…Indica rice accounts for more than 70% of world rice production (2) and is genetically much more diverse than japonica rice (3). Genomic studies have established that indica rice can be further subdivided into two major varietal groups, indica I and indica II, which have been independently bred and widely cultivated in China and Southeast Asia, respectively (4). Hybrids between these groups usually show strong heterosis, which provided the basis for the great success of hybrid rice in several countries, including China and the United States.…”