Heterosis in maize (Zea mays, L.): characterization of heterotic quantitative trait loci (QTL) for agronomic traits in near isogenic lines (NILs) and their testcrosses

In a previous study on maize (Zea mays, L.) several quantitative trait loci (QTL) showing high dominance-additive ratio for agronomic traits were identified in a population of recombinant inbred lines derived from B73 × H99. For four of these mapped QTL, namely 3.05, 4.10, 7.03 and 10.03 according to their chromosome and bin position, families of near-isogenic lines (NILs) were developed, i.e., couples of homozygous lines nearly identical except for the QTL region that is homozygote either for the allele provided by B73 or by H99. For two of these QTL (3.05 and 4.10) the NILs families were produced in two different genetic backgrounds. The present research was conducted in order to: (i) characterize these QTL by estimating additive and dominance effects; (ii) investigate if these effects can be affected by genetic background, inbreeding level and environmental growing conditions (low vs. high plant density). The six NILs’ families were tested across three years and in three Experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two plant densities (4.5 and 9.0 plants m-2). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits, especially for grain yield per plant and its component traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and plant density were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using NILs’ families and their crosses as base materials.

Fine Mapping of qroot-yield-1.06, a QTL for Root, Plant Vigor and Yield in Maize

Root-yield-1.06 is a major QTL affecting root system architecture (RSA) and other agronomic traits in maize. The effect of this QTL has been evaluated with the development of near isogenic lines (NILs) differing at the QTL position. The objective of this study was to fine map qroot-yield-1.06 by marker-assisted searching for chromosome recombinants in the QTL interval and concurrent root phenotyping in both controlled and field conditions, through successive generations. Complementary approaches such as QTL meta-analysis and RNA-seq were deployed in order to help prioritizing candidate genes within the QTL target region. Using a selected group of genotypes, field based root analysis by ‘shovelomics’ enabled to accurately collect RSA information of adult maize plants. Shovelomics combined with software-assisted root imaging analysis proved to be an informative and relatively highly automated phenotyping protocol. A QTL interval mapping was conducted using a segregating population at the seedling stage grown in controlled environment. Results enabled to narrow down the QTL interval and to identify new polymorphic markers for MAS in field experiments. A collection of homozygous recombinant NILs was developed by screening segregating populations with markers flanking qroot-yield-1.06. A first set of lines from this collection was phenotyped based on the adapted shovelomics protocol. QTL analysis based on these data highlighted an interval of 1.3 Mb as completely linked with the target QTL but, a larger safer interval of 4.1 Mb was selected for further investigations. QTL meta-analysis allows to synthetize information on root QTLs and two mQTLs were identified in the qroot-yield-1.06 interval. Trascriptomics analysis based on RNA-seq data of the two contrasting QTL-NILs, confirmed alternative haplotypes at chromosome bin 1.06. qroot-yield-1.06 has now been delimited to a 4.1-Mb interval, and thanks to the availability of additional untested homozygous recombinant NILs, the potentially achievable mapping resolution at qroot-yield-1.06 is c. 50 kb.

QTL mapping identifies novel major loci for ear fasciation, ear prolificacy and tillering in maize (ZEA MAYS L.)

Maize ear fasciation originates from excessive or abnormal proliferation of the ear meristem and usually manifests as multiple-tipped ear, ear flatness and/or disordered kernel arrangement. Ear prolificacy expresses as multiple ears per node. Both traits can affect grain yield. In this study, the genetic control of the two traits was analyzed using two recombinant inbred lines (RIL) populations (B73 × Lo1016 and Lo964 × Lo1016) with Lo1016 and Lo964 as donors of ear fasciation and prolificacy, respectively. Four ear fasciation-related traits (ear fasciation, kernel distribution and ear ovality indexes and ratio of ear diameters), number of kernel rows, ear prolificacy and number of tillers were phenotyped in multi-year field experiments. Ear fasciation traits and number of kernel rows showed relatively high heritability (h2 > 0.5) except ratio of ear diameters, and showed correlation. Prolificacy and tillering h2 ranged 0.41 - 0.78 and did not correlate. QTL mapping identified four QTL for ear fasciation, on chr. 1 (two QTLs), 5 and 7, the latter two overlapping with QTLs for number of kernel rows. However, the strongest effect QTL for number of kernel rows mapped on chr. 2 independently from ear fasciation. Four and five non-overlapping QTLs were mapped for ear prolificacy and tillering, respectively. Two ear fasciation QTLs from this study, qFas1.2 and qFas7, overlapped with formerly known fasciation QTLs and spanned candidate genes expressed in ear meristems namely compact plant2 and ramosa1. Our study identified novel ear fasciation, ear prolificacy and tillering loci which are unexpectedly still segregating in elite maize materials, and provides foundation for genomics-assisted breeding for yield components