Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
Rice Research Department, The National Center for Applied Research on Rural Development (FOFIFA), Antananarivo, Madagascar.
PLoS One. 2022 May 18;17(5):e0262707. doi: 10.1371/journal.pone.0262707. eCollection 2022.
Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers. Consequently, rice productivity remains low and the gap between rice production and consumption is widening at the national level. This study evaluates genetic resources imported from the IRRI rice gene bank to identify potential donors and loci associated with low soil fertility tolerance (LFT) that could be utilized in improving rice yield under local cultivation conditions. Accessions were grown on-farm without fertilizer inputs in the central highlands of Madagascar. A Genome-wide association study (GWAS) identified quantitative trait loci (QTL) for total panicle weight per plant, straw weight, total plant biomass, heading date and plant height. We detected loci at locations of known major genes for heading date (hd1) and plant height (sd1), confirming the validity of GWAS procedures. Two QTLs for total panicle weight were detected on chromosomes 5 (qLFT5) and 11 (qLFT11) and superior panicle weight was conferred by minor alleles. Further phenotyping under P and N deficiency suggested qLFT11 to be related to preferential resource allocation to root growth under nutrient deficiency. A donor (IRIS 313-11949) carrying both minor advantageous alleles was identified and crossed to a local variety (X265) lacking these alleles to initiate variety development through a combination of marker-assisted selection with selection on-farm in the target environment rather than on-station as typically practiced.
水稻（Oryza sativa L.）是马达加斯加的主食，其人均稻米消费量居世界首位。马达加斯加的水稻主要种植在小农户的土地上，这些土地肥力低，缺乏化肥等外部投入。因此，水稻的生产力仍然很低，国家一级的稻米生产和消费之间的差距正在扩大。本研究评估了从国际水稻研究所（IRRI）水稻基因库进口的遗传资源，以确定与耐低土壤肥力（LFT）相关的潜在供体和基因座，这些供体和基因座可用于在当地种植条件下提高水稻产量。在马达加斯加中部高地，没有化肥投入，在农场种植了种质。全基因组关联研究（GWAS）鉴定了每个植株总穗重、稻草重、总植物生物量、抽穗期和株高的数量性状位点（QTL）。我们在已知主基因（hd1 和 sd1）的位置检测到了与抽穗期和株高相关的基因座，证实了 GWAS 程序的有效性。在染色体 5（qLFT5）和 11（qLFT11）上检测到两个总穗重的 QTL，并且次要等位基因赋予了更好的穗重。在 P 和 N 缺乏下的进一步表型分析表明，qLFT11 与在养分缺乏下优先将资源分配给根生长有关。鉴定到一个携带两个有利的次要等位基因的供体（IRIS 313-11949），并与缺乏这些等位基因的当地品种（X265）杂交，通过标记辅助选择与目标环境中的田间选择相结合，而不是像通常那样在站台上进行选择，从而启动品种开发。
